Abstract: With the development of economy and society and the advancement of urbanization in China, new challenges have been brought to rural governance. The report of the Nineteenth National Congress of the Communist Party of China pointed out that we should strengthen the basic work at the grass-roots level in rural areas and improve the rural governance system which combines autonomy, rule of law and rule of virtue, which provides a guide for the modernization of the rural governance system in the new era. This paper expounds the role and dialectical relationship of autonomy, rule of law and rule of virtue in the rural governance system, summarizes Chengdu practice in exploring the combination of autonomy, rule of law and rule of virtue, summarizes the experience of Chengdu practice, reveals the value of Chengdu practice, and puts forward the path choice of the rural governance system combining autonomy, rule of law and rule of virtue.