Multilevel model is a statistical model based on hierarchy structure data form, can not only dig the influence of different hierarchical variables on county economy growth but also analyze the differences in county economy growth. This paper builds three-level development model based on time-countycity to study the influential factors of the perspective of residents’ living level, industrial development, agricultural development, traffic development, investment situation and so on on county economy growth difference of Yunnan Province. Economic gross is determined by initial level and economic growth speed and the results show that the initial level is significantly affected by per capita vegetable output, per capita fixed assets investment and so on at city level, and that growth speed is significantly affected by highway intensity at city level.