Rural household livelihood research of ethnic minorities is urgent to the development of ethnic areas in China and achieve the world poverty reduction goal. To improve ethnic rural household livelihood, it is fundamental to figure out what are the types, characteristics as well as impact factors of their livelihood strategies. In the study, we explored the household livelihood strategy choices and livelihood diversity of the main ethnic minorities (Tujia and Miao) in Chongqing, as well as how livelihood capitals impact livelihood strategy through methods of clustering, livelihood diversity index and multiple logistic regression under the framework of sustainable livelihood approach. The results show that: (1) Full-time job, both full-time and part-time job, part-time agriculture, part-time job and subsidized livelihood strategy are livelihood strategies adopted by Tujia and Miao rural households in Chongqing, China. (2) The characteristics of the identified livelihood strategies are diversified and various in natural, financial, human and finance capital. (3) A number of livelihood capitals impact the way that household choose their livelihood strategies, but the livelihood capitals have no significant impact on the livelihood diversity. By detailed analysis of the characteristic of rural ethnic household livelihood strategy, especial livelihood diversity, the research enriched sustainable livelihood literature and provided useful information for policymakers and practitioners in designing effective programs for regional sustainable development and ecological protection.