Abstract: Non-point source pollution is required to consider the whole process factors of generation, formation, and regulation. In this study, the risk assessment system was constructed to evaluate the non-point source pollution in the Three Gorges Reservoir Area using an analytic hierarchy process. Taking the availability of data as an essential source, an operable index system was then proposed to overcome the excessive indicators of individual risk using Weber-Fechner. Finally, the horizontal and vertical lists of pollution control were determined for the decision-making. The result showed that agricultural non-point source pollution was predicted as the middle-risk level in the study area. The higher scores of risks were found in the Yiling District in Hubei Province and Nanan District in Chongqing Municipality. The next high-risk scores were distributed in Dadukou District, Shapingba District, Wuxi County in Chongqing Municipality and Xingshan County, Zigui County in Hubei Province, and the following were Kaizhou District, Wanzhou District, Fengdu County, and Yunyang County in Chongqing Municipality. The influencing indexes were obtained as fertilizer intensity, livestock/poultry breeding intensity, rainfall erosion, and environmental protection investment index in the risk system of agricultural non-point source pollution. The ratio between the risk scores of fertilizer intensity and livestock/poultry breeding intensity index accounted for 79% of the total risk scores of press indexes. By contrast, the ratios were more than 90% in Wuxi, Badong, and Wushan County. The average ratios of risk score were 32%, 25%, 24%, and 19%, respectively, for the stress, transformation, state, and governance index to the comprehensive one. Among them, the stress index still occupied the largest proportion of the risk score. Fertilizer intensity was higher in Nanan District, Dadukou District of Chongqing Municipality, and the counties in Hubei Province. Some suggestions were then proposed to improve the fertilization of fruit trees. The relatively high intensity of livestock and poultry breeding was concentrated mainly in Yunyang County, Kaizhou District, Wuxi County, Wushan County in Chongqing Municipality, and the counties in Hubei Province. Particularly, it was necessary to improve the waste treatment of pigs and sheep. In addition, the planting structure was required to adjust reasonably to increase the investment in environmental protection. In the vertical lists of pollution control, Yiling and Nanan District should be given priority to the agricultural non-point source pollution control, where the priority areas of river water quality control were Dadukou, Jiulongpo District, and the counties in Hubei Province. In the horizontal lists of pollution control, the pollution control factors in most counties were fertilizer reduction and livestock breeding control. More attention should be paid to fertilizer reduction in the upstream and downstream areas, while the pollution prevention and control caused by livestock and poultry breeding in the middle reaches. Furthermore, the slope length index of each county was evaluated, according to the average value of 0.026. Soil erodibility of each county was chosen from 0.015 to 0.019 ·hm²·h/(MJ·mm·hm²) for the better performance of risk assessment. This finding can provide a strong reference for the policy formulation of agricultural non-point source pollution in the Three Gorges reservoir area.