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The modernization process of agriculture has led to serious agricultural non-point source pollution. It is a new direction to study the evaluation framework of agricultural production efficiency by including the ecological environment effect of agriculture. Agricultural eco-environmental efficiency which combines both economic and ecological performance is a valid way for agricultural sustainability analysis. Based on the non-radial and non-angle SBM-DEA model and the directional distance function, the agricultural eco-environmental efficiency of the Three Gorges Reservoir area in Chongqing during the period from 2003 to 2015 was investigated. The marginal price of agricultural non-point source pollution was estimated by introducing the shadow price cost of emission reduction. The results showed that: 1) During the period of 2006 to 2015, the agro-ecological environment efficiency of the Three Gorges Reservoir area in Chongqing tended to increase steadily, but the overall level was low；2) The input and output of each district (county) were needed to change to optimize the efficiency of agro-ecological environment. The areas with high agro-ecological environment were concentrated in the urban core area and the urban fringe of the reservoir, while the eco-environmental efficiency of the low mountain and hill area, parallel ridge valley area, mountainous area in the hinterland and surrounding mountain area in the hinterland were relatively low; 3) From the reasons of the efficiency loss, the excessive use of chemical fertilizers and pesticides and their corresponding adverse ecological and environmental effects were outstanding, mainly due to the inefficiency of agricultural investment and the inefficiency of undesired output; 4) The shadow prices of agricultural non-point source pollution in Dadukou, Nan’an, Jiangbei, Beibei and Yubei area were at the forefront, and the pollution abatement space was small, therefor, the task of reducing agricultural non-point source pollution should be commissioned. Fengdu, Kaixian and Wanxian district’s shadow prices of agricultural non-point source pollution emission were low, thus those three areas should be assigned to agricultural non-point source pollution reduction. Chongqing section of Three Gorges Reservoir Area had an enormous potential for reduction of agricultural non-point source pollution and for the decrease of resource inputs to enhance the agricultural eco-environmental efficiency. Agricultural eco-environmental efficiency evaluation plays an important role in promoting agriculture ecological and sustainable development. The eco-environmental efficiency optimization provides further implications on resource and environmental protection strategies in Chongqing section of Three Gorges Reservoir Area. Meanwhile, we should evaluate agricultural eco-environmental efficiency according to resources endowment, factor substitution, adverse impact on ecology and environment and consider the regional development and different stages, we should promote differently the development of ecological agriculture. [ABSTRACT FROM AUTHOR]