The browser DOM automatically binds the first 1000 option, So if you are trying to hide/show it will be applicable only on the first 1000 option.
As workaround has to fill the select with only the filtered options not hide all and show the filtered.
To do this hide the village select and add an empty select filtered only fill it with the filtered and you can use a selector to filter better than the loop I enhanced your code.
But still I don’t suggest to have a huge select better to handle them with ajax and to get only the filter options to the page
This is a sample code:
$(function(){
$("#village ").hide();
});
function checkVillage() {
$("#filtered").html($("#village option[data-id='[" + $('#district').val() + "]"));
if ($('#village :selected').is(':hidden')) {
$('#village').val('');
}
}
$('#district').on('change', function() {
checkVillage();
});<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
District
<select id="district" name="d" required >
<option value="">select</option>
<option value="61">Rukum</option>
<option value="62">Salyan</option>
<option value="63">Rolpa</option>
<option value="64">Pyuthan</option>
<option value="65">Dang</option></select>
</select>
<br><br>
Village
<select id="village" name="v" required>
<option data-id="[61]" value="3286">Gotamkot</option>
<option data-id="[61]" value="3287">Ghetma</option>
<option data-id="[61]" value="3288">Hukam</option>
<option data-id="[61]" value="3290">Jhula</option>
<option data-id="[61]" value="3291">Kanda</option>
<option data-id="[61]" value="3293">Khara</option>
<option data-id="[61]" value="3294">Kholagaun</option>
<option data-id="[61]" value="3295">Kol</option>
<option data-id="[61]" value="3297">Magma</option>
<option data-id="[61]" value="3298">Mahat</option>
<option data-id="[61]" value="3299">Morawang</option>
<option data-id="[61]" value="3301">Musikot Khalanga</option>
<option data-id="[61]" value="3302">Nuwakot</option>
<option data-id="[61]" value="3304">Pokhara</option>
<option data-id="[61]" value="3305">Purtim Kanda</option>
<option data-id="[61]" value="3307">Pyugha</option>
<option data-id="[61]" value="3308">Rangsi</option>
<option data-id="[61]" value="3310">Rugha</option>
<option data-id="[61]" value="3311">Sankha</option>
<option data-id="[61]" value="3312">Simli</option>
<option data-id="[61]" value="3313">Sisne</option>
<option data-id="[61]" value="3315">Syalakhadi</option>
<option data-id="[61]" value="3316">Syalapakha</option>
<option data-id="[61]" value="3275">Aathbis Dandagaun</option>
<option data-id="[61]" value="3277">Arma</option>
<option data-id="[61]" value="3278">Baphikot</option>
<option data-id="[61]" value="3279">Bhalakachha</option>
<option data-id="[61]" value="3280">Bijeswori (Chaurjhari)</option>
<option data-id="[61]" value="3282">Chaukabang</option>
<option data-id="[61]" value="3283">Chunwang</option>
<option data-id="[61]" value="3284">Duli</option>
<option data-id="[61]" value="3276">Aathbis Kot</option>
<option data-id="[61]" value="3281">Chhiwang</option>
<option data-id="[61]" value="3285">Garayala</option>
<option data-id="[61]" value="3289">Jangh</option>
<option data-id="[61]" value="3292">Kankri</option>
<option data-id="[61]" value="3296">Kotjahari</option>
<option data-id="[61]" value="3300">Muru</option>
<option data-id="[61]" value="3303">Pipal</option>
<option data-id="[61]" value="3306">Pwang</option>
<option data-id="[61]" value="3309">Ranmamaikot</option>
<option data-id="[61]" value="3314">Sobha</option>
<option data-id="[61]" value="3317">Taksera</option>
<option data-id="[62]" value="3177">Badagaun</option>
<option data-id="[62]" value="3178">Bafukhola</option>
<option data-id="[62]" value="3179">Bajh Kanda</option>
<option data-id="[62]" value="3180">Bangad Bame</option>
<option data-id="[62]" value="3181">Bhalchaur</option>
<option data-id="[62]" value="3182">Chande</option>
<option data-id="[62]" value="3183">Chhayachhetra</option>
<option data-id="[62]" value="3184">Damachaur</option>
<option data-id="[62]" value="3185">Dadagaun</option>
<option data-id="[62]" value="3186">Darmakot</option>
<option data-id="[62]" value="3187">Devsthal</option>
<option data-id="[62]" value="3188">Ghanjari Pipal</option>
<option data-id="[62]" value="3189">Dhakadam</option>
<option data-id="[62]" value="3190">Dhanbang</option>
<option data-id="[62]" value="3191">Hiwalcha</option>
<option data-id="[62]" value="3192">Korbang Jhimpe</option>
<option data-id="[62]" value="3193">Jimali</option>
<option data-id="[62]" value="3194">Kabhrechaur</option>
<option data-id="[62]" value="3195">Kajeri (Malneta)</option>
<option data-id="[62]" value="3196">Kalagaun</option>
<option data-id="[62]" value="3197">Kalimati Kalche</option>
<option data-id="[62]" value="3198">Karagithi</option>
<option data-id="[62]" value="3199">Kavra</option>
<option data-id="[62]" value="3200">Khalanga</option>
<option data-id="[62]" value="3201">Kotbara</option>
<option data-id="[62]" value="3202">Ktmoula</option>
<option data-id="[62]" value="3203">Kubhinde Daha</option>
<option data-id="[62]" value="3204">Laxmipur</option>
<option data-id="[62]" value="3205">Lekhpokhara</option>
<option data-id="[62]" value="3206">Majh Kharka</option>
<option data-id="[62]" value="3207">Marke</option>
<option data-id="[62]" value="3208">Marmapari Kanda</option>
<option data-id="[62]" value="3209">Mulkhola</option>
<option data-id="[62]" value="3211">Phalabang</option>
<option data-id="[62]" value="3212">Pipal Neta</option>
<option data-id="[62]" value="3213">Kalimati Rampur</option>
<option data-id="[62]" value="3214">Rim</option>
<option data-id="[62]" value="3215">Saijuwal Takura</option>
<option data-id="[62]" value="3216">Sarpani Garpa</option>
<option data-id="[62]" value="3217">Sibaratha</option>
<option data-id="[62]" value="3218">Siddheswor</option>
<option data-id="[62]" value="3219">Singwang</option>
<option data-id="[62]" value="3220">Suikot</option>
<option data-id="[62]" value="3221">Syanikhal</option>
<option data-id="[62]" value="3222">Tharmare</option>
<option data-id="[62]" value="3223">Tribeni</option>
<option data-id="[62]" value="4137">Nigalchula</option>
<option data-id="[63]" value="3224">Ares</option>
<option data-id="[63]" value="3225">Bhawang</option>
<option data-id="[63]" value="3226">Bhirul</option>
<option data-id="[63]" value="3228">Dhawang</option>
<option data-id="[63]" value="3229">Dubidada</option>
<option data-id="[63]" value="3230">Dubring</option>
<option data-id="[63]" value="3232">Fagaam</option>
<option data-id="[63]" value="3233">Gaam</option>
<option data-id="[63]" value="3235">Gairigaun</option>
<option data-id="[63]" value="3236">Ghartigaun</option>
<option data-id="[63]" value="3237">Ghodagaun</option>
<option data-id="[63]" value="3239">Harjung</option>
<option data-id="[63]" value="3240">Jedwang</option>
<option data-id="[63]" value="3242">Jankot</option>
<option data-id="[63]" value="3243">Jauli Pokhari</option>
<option data-id="[63]" value="3244">Jelwang</option>
<option data-id="[63]" value="3245">Jhenam</option>
<option data-id="[63]" value="3247">Jungar</option>
<option data-id="[63]" value="3248">Korchawang</option>
<option data-id="[63]" value="3249">Kareti</option>
<option data-id="[63]" value="3251">Khungri</option>
<option data-id="[63]" value="3252">Kotgaun</option>
<option data-id="[63]" value="3253">Kureli</option>
<option data-id="[63]" value="3255">Masina</option>
<option data-id="[63]" value="3256">Mijhing</option>
<option data-id="[63]" value="3258">Pachhaiwang (Ghartigaun)</option>
<option data-id="[63]" value="3259">Pakhapani</option>
<option data-id="[63]" value="3260">Pang</option>
<option data-id="[63]" value="3262">Rangsi</option>
<option data-id="[63]" value="3263">Rank</option>
<option data-id="[63]" value="3264">Sakhi</option>
<option data-id="[63]" value="3266">Sirpa</option>
<option data-id="[63]" value="3267">Siuri</option>
<option data-id="[63]" value="3269">Tewang</option>
<option data-id="[63]" value="3270">Thawang</option>
<option data-id="[63]" value="3271">Uwa</option>
<option data-id="[63]" value="3273">Whama</option>
<option data-id="[63]" value="3274">Wot</option>
<option data-id="[63]" value="3227">Budagaun</option>
<option data-id="[63]" value="3231">Eriwang</option>
<option data-id="[63]" value="3234">Gajul</option>
<option data-id="[63]" value="3238">Gumchal</option>
<option data-id="[63]" value="3241">Jaimakasala</option>
<option data-id="[63]" value="3246">Jinawang</option>
<option data-id="[63]" value="3250">Khumel</option>
<option data-id="[63]" value="3254">Liwang</option>
<option data-id="[63]" value="3257">Nuwagaun</option>
<option data-id="[63]" value="3261">Rangkot</option>
<option data-id="[63]" value="3265">Seram</option>
<option data-id="[63]" value="3268">Talawang</option>
<option data-id="[63]" value="3272">Wadachaur</option>
<option data-id="[64]" value="3128">Akhra</option>
<option data-id="[64]" value="3129">Badikot</option>
<option data-id="[64]" value="3130">Bangesal</option>
<option data-id="[64]" value="3131">Baraula</option>
<option data-id="[64]" value="3132">Barjiwang</option>
<option data-id="[64]" value="3133">Belwas</option>
<option data-id="[64]" value="3134">Bhingri</option>
<option data-id="[64]" value="3135">Bijaya Nagar</option>
<option data-id="[64]" value="3136">Bijubar</option>
<option data-id="[64]" value="3137">Bijuli</option>
<option data-id="[64]" value="3138">Chuja (Muna)</option>
<option data-id="[64]" value="3139">Damri</option>
<option data-id="[64]" value="3140">Dangbang</option>
<option data-id="[64]" value="3141">Dankhakwadi</option>
<option data-id="[64]" value="3142">Dharampani</option>
<option data-id="[64]" value="3143">Dharmawati</option>
<option data-id="[64]" value="3144">Dhobaghat(Udaypurkot)</option>
<option data-id="[64]" value="3145">Dhowang</option>
<option data-id="[64]" value="3146">Dhungegadi</option>
<option data-id="[64]" value="3147">Gothiwang</option>
<option data-id="[64]" value="3148">Hansapur</option>
<option data-id="[64]" value="3149">Jumrikanda</option>
<option data-id="[64]" value="3150">Khaira</option>
<option data-id="[64]" value="3151">Khawang</option>
<option data-id="[64]" value="3152">Khung</option>
<option data-id="[64]" value="3153">Kochiwang</option>
<option data-id="[64]" value="3154">Ligha</option>
<option data-id="[64]" value="3155">Liwang</option>
<option data-id="[64]" value="3156">Lung</option>
<option data-id="[64]" value="3157">Manjhakot</option>
<option data-id="[64]" value="3158">Maranthana</option>
<option data-id="[64]" value="3159">Markawang</option>
<option data-id="[64]" value="3160">Narikot</option>
<option data-id="[64]" value="3161">Naya Gaun</option>
<option data-id="[64]" value="3162">Okharkot</option>
<option data-id="[64]" value="3163">Pakala</option>
<option data-id="[64]" value="3164">Phopli</option>
<option data-id="[64]" value="3165">Puja</option>
<option data-id="[64]" value="3166">Pyuthan Khalanga</option>
<option data-id="[64]" value="3167">Rajbara</option>
<option data-id="[64]" value="3168">Ramdi</option>
<option data-id="[64]" value="3169">Ruspur Kot</option>
<option data-id="[64]" value="3170">Sari</option>
<option data-id="[64]" value="3171">Syauliwang</option>
<option data-id="[64]" value="3172">Swargadwari</option>
<option data-id="[64]" value="3173">Torwang</option>
<option data-id="[64]" value="3174">Tiram</option>
<option data-id="[64]" value="3175">Tusara</option>
<option data-id="[64]" value="3176">Wangemaroth</option>
<option data-id="[65]" value="3088">Shantinagar (Amritpur)</option>
<option data-id="[65]" value="3089">Baghmare</option>
<option data-id="[65]" value="3090">Bela</option>
<option data-id="[65]" value="3091">Bijauri</option>
<option data-id="[65]" value="3092">Chaulahi</option>
<option data-id="[65]" value="3093">Dhanori</option>
<option data-id="[65]" value="3094">Dharna</option>
<option data-id="[65]" value="3095">Dhikpur</option>
<option data-id="[65]" value="3096">Duruwa</option>
<option data-id="[65]" value="3097">Gabardiya</option>
<option data-id="[65]" value="3098">Gadhawa</option>
<option data-id="[65]" value="3099">Gangapraspur</option>
<option data-id="[65]" value="3100">Goltakuri</option>
<option data-id="[65]" value="3101">Halwar</option>
<option data-id="[65]" value="3102">Hansipur</option>
<option data-id="[65]" value="3103">Hapur (Basantpur)</option>
<option data-id="[65]" value="3104">Hekuli</option>
<option data-id="[65]" value="3105">Kabhre</option>
<option data-id="[65]" value="3106">Koilabas</option>
<option data-id="[65]" value="3107">Lalmatiya</option>
<option data-id="[65]" value="3108">Laxmipur</option>
<option data-id="[65]" value="3109">Loharpani</option>
<option data-id="[65]" value="3110">Manpur</option>
<option data-id="[65]" value="3111">Narayanpur</option>
<option data-id="[65]" value="3112">Panchakule</option>
<option data-id="[65]" value="3113">Pawan Nagar</option>
<option data-id="[65]" value="3114">Phulbari</option>
<option data-id="[65]" value="3115">Purandhara</option>
<option data-id="[65]" value="3116">Rajpur</option>
<option data-id="[65]" value="3117">Rampur</option>
<option data-id="[65]" value="3118">Saidha</option>
<option data-id="[65]" value="3119">Satbariya</option>
<option data-id="[65]" value="3120">Saudiyar</option>
<option data-id="[65]" value="3121">Sisahaniya</option>
<option data-id="[65]" value="3122">Sonpur</option>
<option data-id="[65]" value="3123">Syuja</option>
<option data-id="[65]" value="3124">Tarigaun</option>
<option data-id="[65]" value="3125">Tribhuvan Nagar Municipality</option>
<option data-id="[65]" value="3126">Tulsipur Municipality</option>
<option data-id="[65]" value="3127">Urahari</option>
<option data-id="[65]" value="4138">Sreegaun</option>
</select>
<select id="filtered"></select>