Based on the theory and method of water footprint, the paper calculated and analyzed the water footprint of agricultural water consumption in Yunnan province from 2000 to 2008.According to the results of water footprint calculation and the related input and output indicators,this paper established DEA model so as to evaluate the situation of sustainable development of agricultural water resources and agricultural economic system in Yunnan province in nine years,and quantitatively analyzed the relative carrying capacity of agricultural water resources in Yunnan province. The results showed that ①during period of 2000 to 2003, 2006 to 2008, Yunnan province was effective based on DEA, which meant that the relative performance of development between the exploitation and utilization of agricultural water resources and the economic development achieved to the optimal, the technology and economy of scale were also effective;②In Yunnan province, the relative bearing capacity index of water resources was less than 1 in 2004 and 2005, DEA of Yunnan province is ineffective;③the growth of sustainable development of Yunnan province is relatively slow and presented the weakly track of sustainable development.