Abstract: The control of agricultural non-point source pollution is not only an effective way to achieve a healthy agricultural production environment but also a key grip for the Yangtze River Economic Belt to achieve quality improvement, efficiency upgrading, and green development, which is related to the realization of the strategic goal of the development of the Yangtze River Economic Belt. Taking the implementation of the development strategy of the Yangtze River Economic Belt in the upstream area of the Yangtze River (Chongqing, Sichuan, Guizhou, Yunnan) in 2015 as a quasi-natural experiment, the synthetic control method was used to evaluate the impact of the development strategy of the Yangtze River Economic Belt on the efficiency of agricultural ecological environment in this region. The results show that the development strategy of the Yangtze River Economic Belt promotes the efficiency of the agricultural ecological environment in the upstream area, and increases with the deepening of the development strategy of the Yangtze River Economic Belt. The analysis of regional heterogeneity shows that the development strategy has promoted the efficiency of the agricultural ecological environment in Chongqing, Sichuan, Guizhou, and Yunnan, and achieved the policy goal of effective control of agricultural and rural non-point source pollution in the Yangtze River Economic Belt by 2020. Therefore, when promoting the efficiency of the agricultural ecological environment, the government should pay more attention to improving the efficiency of fiscal and environmental protection expenditure in the Yangtze River Economic Belt, increasing revenue and reducing expenditure, so as to achieve the expected income goals of policymakers and farmers.