Abstract: Multidimensional poverty problem of farmers in the poverty-stricken ethnic minority regions is widespread. Analyzing this problem is of great significance for the purpose of formulating poverty reduction policies scientifically. Applying Sen’s Capability Approach and based on three regions of Southern Xinjiang as examples, this paper built a multidimensional poverty index system of farmers to evaluate the level of multidimensional poverty and the contribution of each dimension of multidimensional poverty using A-F method and to explore the cause of poverty. Results show that 1) in these three regions of Southern Xinjiang there are not only serious poverty problem from income perspective, but also from perspectives of education, health, sanitation facility, cooking fuel, water safety; 2) the proportion of three and above index deprived population reaches 89.1% and the level of multidimensional poverty reaches 38.9%; 3) the multidimensional poverty is more serious than income poverty; 4) the multidimensional poverty rates continue to decline with the increasing of dimensions, but the depth of poverty gradually deepens; and 5) the contribution of education, income and health poverty to multidimensional poverty index reach respectively 35.73%, 19.37% and 11.19% respectively and become the main source of multidimensional poverty. This paper suggests that the future focus of poverty reduction needs to invest heavily in education, to increase farmers’ income, to increase investment to medical and health security, to education farmers with new ideas, and to establish multidimensional poverty precision targeting mechanism.