Abstract: SBM model was used to measure the agricultural production efficiency of each city in Yunnan province using the 2017 Yunnan Statistical Yearbook date. Then this paper will evaluate the factors affecting agriculture production efficiency in 16 cities in Yunnan Province by factor analysis. We compare and analyze the scores and the rankings of three common factors which include agricultural input factor, development level factor and industrial structure factor. The results show that the three types of influencing factors represented by the three common factors have different effects on the agricultural production efficiency of each city. Then 16 cities are divided into six categories by cluster analysis method, and the agricultural production in each area is analyzed. The paper also presents the suggestions about the development of agriculture in 16 cities in Yunnan Province.