Abstract: Using Malmquist index method of the nonparametric DEA Models, this paper calculated the efficiency of tobacco agricultural science and technology innovation during 2006 to 2015 period in 9 counties of Qujing, and compared the inter annual fluctuation of tobacco total factor productivity and difference from different tobacco planting area nearly a decade in Qujing. The results show that: in 2006-2015,the average growth rate of tobacco agricultural science and technology innovation efficiency was 5% in Qujing, the average growth rate of technical progress was about 4.8%.From 9 counties, the average total factor productivity of tobacco agricultural production is above 1 in Qujing. In addiction to Xuanwei tobacco agricultural science and technology innovation growth rate fell 2%, the other counties tobacco agricultural science and technology innovation efficiency growth rate achieved positive growth, especially the Qilin district grew the fastest, reaching 11%. Generally speaking, technical progress was the main factor to promote the efficiency of tobacco agricultural science and technology innovation in Qujing.