Three South Xinjiang Districts, which is the special poverty area of extensive poverty alleviation, is marked by the features of the borders, the nationality and the closure. To study the dynamic changes and influencing factors of this area’s multidimensional poverty, the paper is based on AF multidimensional poverty method and by dint of binary choice model and ranking model for panel data to empirical analyze the survey data of 2011-2012 of Organization of National Bureau of Statistics Rural Household. The influence of human capital, physical capital and social capital on multidimensional poverty is estimated and the microscopic action mechanism of village-level poverty-alleviation development plan in poverty-alleviation is further discussed. Results show that the condition of multidimensional poverty is better improved, and its spatial difference is gradually reduced. The variables of human capital, physical capital and social capital have a impact on multidimensional poverty, compared with the other two, social capital has a significant payoff for reducing the farmers’ multidimensional poverty, and village-level poverty-alleviation development plan plays a poverty-decreasing role via farmer’s human capital on microscopic level. So we should encourage the poor to improve the poverty conditions by taking an active part in professional economic cooperation organizations to accumulate human capital and social capital and to boost self-development capacity. Meanwhile, grassroots poverty-alleviation work should be effectively implemented.