Abstract: With the promotion of rural revitalization strategy, scientific and reasonable selection of modern agricultural leading industries is a fundamental path to achieving rural industrial prosperity, rural economic development, and eliminating rural poverty, which is of great practical significance to realize the overall revitalization of rural areas and to accelerate the sustainable development of economic society. Based on the relevant theories of industrial economics and the basic requirements, criteria and construction principles of leading industry selection, and combining with the actual situation of agriculture in the Three Gorges Reservoir area, this paper designed a selection index system of modern agricultural leading industries by the Analytic Hierarchy Process (AHP) and the weighted sum method to calculate and analyze the indices in Wanzhou district of Chongqing, and discussed the development focus and cultivation direction of modern agricultural leading industries. Results show that: 1) from the single index perspective, among the 14 types of modern agricultural industries, Chinese herbal medicine, which ranked the second in the demand elasticity of income and the growth rate of unit output value, lamb, which ranked the first in the growth rate of industrial output value, and pork, which ranked the fourth in industrial concentration, per capita output value coefficient and regional aggregated advantage index, are not in the priority cultivation list; and 2) from the comprehensive index perspective, the ranking in descending order are: tea, tobacco, dairy, forestry, oilseeds, aquaculture, food crops, Chinese herbal medicine, pork, lamb, fruits, vegetables, beef and poultry eggs. In summary, this paper suggests that the Government should give priority to the cultivation and development of six types of modern agricultural leading industries, including tea, tobacco, dairy, forestry, oilseeds, and aquaculture.