Background

There are five levels of Autonomous administrative divisions in China, namely

1. Province – Autonomous Regions
2. Prefecture – Autonomous Prefectures
3. County – Autonomous Counties/Banners, Ethnic Districts
4. Township – Ethnic Town/Township/Sumu
5. Village – Ethnic Village

Strictly speaking, “Ethnic” administrative divisions in level 3-5 are not considered “autonomous” by law. However, for the purpose of this answer let’s ignore this caveat.

Note 1: This answer deals with Township-level and above only, as there are simply too many villages to sift through!

Note 2: Some three-level deep examples are non-continuous, which I believe are not against the spirit of the question.

Note 3: At county level and above, there are official and established transliteration conventions for place names that originated in languages other than Chinese (example: Kashgar 喀什). However, it is extremely difficult to find such conventions for names of townships. As such, townships are transliterated in Pinyin here (example: Kekeyaer Kirghiz Ethnic Township 科克亚尔柯尔克孜族乡).

UPDATED transliterations for township names from the following sources,

1. NGA GEOnet Names Server (GNS)
2. EKI Place Names Database (KNAB)
3. 中国地名词典 (Zhongguo diming cidian), Shanghai Lexicographical Publishing House, 1990

Note 4: Tacheng Prefecture and Altay Prefecture are administratively under the sub-provincial Ili Kazakh Autonomous Prefecture.

Winners (four-level deep)

Xinjiang Uyghur Autonomous Region (新疆维吾尔自治区) (2)

• Changji Hui Autonomous Prefecture (昌吉回族自治州)

  Mori Kazakh Autonomous County (木垒哈萨克自治县)

  —- Danangou Uzbek Ethnic Township (大南沟乌孜别克族乡)

• Ili Kazakh Autonomous Prefecture (伊犁哈萨克自治州)

  Qapqal Xibe Autonomous County (察布查尔锡伯自治县)

  —- Miliangquan Hui Ethnic Township (米粮泉回族乡)

Honourable mentions (three-level deep)

Xinjiang Uyghur Autonomous Region (新疆维吾尔自治区) (30)

• Kashgar Prefecture (喀什地区)

  Taxkorgan Tajik Autonomous County (塔什库尔干塔吉克自治县)

  —- Kokyar Kirghiz Ethnic Township (科克亚尔柯尔克孜族乡)

• Changji Hui Autonomous Prefecture (昌吉回族自治州)

  Changji City (昌吉市)

  —- Axili Kazakh Ethnic Township (阿什里哈萨克族乡)

  Fukang City (阜康市)

  —- Sangonghe Kazakh Ethnic Township (三工河哈萨克族乡)

  —- Akkol Kazakh Ethnic Township (上户沟哈萨克族乡)

  Hutubi County (呼图壁县)

  —- Tasbaspaldak Kazakh Ethnic Township (石梯子哈萨克民族乡)

  Manas County (玛纳斯县)

  —- Qingshuihe Kazakh Ethnic Township (清水河哈萨克族乡)

  —- Taxihe Kazakh Ethnic Township (塔西河哈萨克族乡)

  —- Hankazitan Kazakh Ethnic Township (旱卡子滩哈萨克族乡)

  Qitai County (奇台县)

  —- Wumachang Kazakh Ethnic Township (五马场哈萨克族乡)

  —- Qorin Kazakh Ethnic Township (乔仁哈萨克族乡)

  —- Daquan Tatar Ethnic Township (大泉塔塔尔族乡)

• Bayingolin Mongol Autonomous Prefecture (巴音郭楞蒙古自治州)

  Yanqi Hui Autonomous County (焉耆回族自治县)

  Hoxud County (和硕县)

  —- Uxxaktal Hui Ethnic Township (乌什塔拉回族乡)

• Ili Kazakh Autonomous Prefecture (伊犁哈萨克自治州)

  Khorgas City (霍尔果斯市)

  —- Iqegaxan Xibe Ethnic Township (伊车嘎善锡伯族乡)

  Yining County (伊宁县)

  —- Yuqunweng Hui Ethnic Township (愉群翁回族乡)

  Huocheng County (霍城县)

  —- Sangong Hui Ethnic Township (三宫回族乡)

  Zhaosu County (昭苏县)

  —- Qagan Us Mongol Ethnic Township (察汗乌苏蒙古族乡)

  —- Xat Kirghiz Ethnic Township (夏特柯尔克孜族乡)

  —- Hosumtuharson Mongol Ethnic Township (胡松图喀尔逊蒙古族乡)

  Tekes County (特克斯县)

  —- Hujirti Mongol Ethnic Township (呼吉尔特蒙古族乡)

  —- Kokterak Kirghiz Ethnic Township (阔克铁热克柯尔克孜族乡)

  Nilka County (尼勒克县)

  —- Hoh Hothor Mongol Ethnic Township (科克浩特浩尔蒙古族乡)

• Tacheng Prefecture (塔城地区)

  Tacheng City

  —- Axili Daur Ethnic Township (阿西尔达斡尔族乡)

  Usu City (乌苏市)

  —- Jirgiltigolin Mongol Ethnic Township (吉尔格勒特郭愣蒙古族乡)

  —- Tablihat Mongol Ethnic Township (塔布勒合特蒙古族乡)

  Emin County (额敏县)

  —- Emalgolin Mongol Ethnic Township (额玛勒郭楞蒙古族乡)

  —- Hujirti Mongol Ethnic Township (霍吉尔特蒙古族乡)

• Altay Prefecture (阿勒泰地区)

  Altay City (阿勒泰市)

  —- Handigati Mongol Ethnic Township (汗德尕特蒙古族乡)

  Burqin County (布尔津县)

  —- Kumkanas Mongol Ethnic Township (禾木哈纳斯蒙古族乡)

Guangxi Zhuang Autonomous Region (广西壮族自治区) (6)

• Liuzhou City (柳州市)

  Rongshui Miao Autonomous County (融水苗族自治县)

  —- Tonglian Yao Ethnic Township (同练瑶族乡)

  —- Gunbei Dong Ethnic Township (滚贝侗族乡)

  Sanjiang Dong Autonomous County (三江侗族自治县)

  —- Tongle Miao Ethnic Township (同乐苗族乡)

  —- Gaoji Miao Ethnic Township (高基苗族乡)

  —- Fulu Yao Ethnic Township (富禄瑶族乡)

• Hechi City (河池市)

  Huanjiang Maonan Autonomous County (环江毛南族自治县)

  —- Xunle Miao Ethnic Township (驯乐苗族乡)

Sichuan Province (四川省) (5)

• Liangshan Yi Autonomous Prefecture (凉山彝族自治州)

  Muli Tibetan Autonomous County (木里藏族自治县)

  —- Eya Nakhi Ethnic Township (俄亚纳西族乡)

  —- Wujiao Mongol Ethnic Township (屋脚蒙古族乡)

  —- Baidiao Miao Ethnic Township (白碉苗族乡)

  —- Xiangjiao Mongol Ethnic Township (项脚蒙古族乡)

  —- Guzeng Miao Ethnic Township (固增苗族乡)

Inner Mongolia Autonomous Region (内蒙古自治区) (3)

• Hulunbuir City (呼伦贝尔市)

  Ewenki Autonomous Banner (鄂温克族自治旗)

  —- Bayan Tal Daur Ethnic Township (巴彦塔拉达斡尔族乡)

  Morin Dawa Daur Autonomous Banner (莫力达瓦达斡尔族自治旗)

  —- Bayan Ewenki Ethnic Township (巴彦鄂温克族乡)

  —- Dulari Ewenki Ethnic Township (杜拉尔鄂温克族乡)

Yunnan Province (云南省) (2)

• Honghe Hani and Yi Autonomous Prefecture (红河哈尼族彝族自治州)

  Hekou Yao Autonomous County (河口瑶族自治县)

  —- Qiaotou Miao and Zhuang Ethnic Township (桥头苗族壮族乡)

  Jinping Miao, Yao, and Dai Autonomous County (金平苗族瑶族傣族自治县)

  —- Zhemi Lahu Ethnic Township (者米拉祜族乡)

Qinghai Province (青海省) (1)

• Haibei Tibetan Autonomous Prefecture (海北藏族自治州)

  Menyuan Hui Autonomous County (门源回族自治县)

  —- Huangcheng Mongol Ethnic Township (皇城蒙古族乡)

Ili Kazakh Autonomous Prefecture is part of the Xinjiang Uyghur Autonomous Region, making Qapqal Xibe Autonomous County a three-level deep autonomous area!