Abstract: This paper makes use of ecological footprint method to set up the structure model of ecological footprint of plateau special feature agricultural product about 30 kinds of agricultural products in Yunnan province, and gets how to make the structure of the plateau special feature agricultural product be optimized by means of substantial evidence analysis of the ecological footprint and production value footprint. The conclusion shows the agricultural product featured the characteristics of highest ecological and economic comprehensive benefits, such as potato and the vegetable, melon and grape, pineapple and banana, apple and pear, orange and sugar, spice crop, chestnut and walnut, birds meat and marine products, need to give priority to develop, and other agricultural products gradually develop. Finally, this paper puts forward suggestions about the structure optimization of plateau special feature agricultural product in Yunnan province..