[Objective] The coupling and coordination relationship between soil and water conservation policy and agricultural eco-efficiency, and its driving factors were analyzed to provide a new perspective and thinking for further understanding of the coordination relationship between soil and water conservation policy and agricultural eco-efficiency. [Methods] An evaluation index system for soil and water conservation policy intensity and agricultural eco-efficiency was established using the Three Gorges reservoir (Chongqing section) as the research area. The coupling coordination degree model, geographical detector model, and ordinary least squares (OLS) regression were used to analyze the coupling relationship between the soil and water conservation policy and agricultural eco-efficiency, and its driving mechanism in the region from 2015 to 2022. [Results] ① There were significant differences in policy intensity and ecological efficiency among regions in the Three Gorges reservoir area (Chongqing section). The maintenance area of soil-conserving human settlements in the Fangshan Hills and parallel ridges and valleys showed strong growth momentum during policy implementation, whereas the rest of the region was relatively stable. The agricultural ecological efficiency of the urban landscape living environment maintenance area was excellent, whereas that of the Wuling Mountain water and soil conservation areas was relatively low, showing an obvious polarization trend. ② The degree of coupling coordination between soil and water conservation policies and agricultural ecological efficiency showed an overall upward trend, and the coordination degree of the urban landscape human settlement environment maintenance area and the Fangshan hilly soil conservation human settlement environment maintenance area was particularly prominent. However, there was a significant imbalance of that in Kaizhou District in the areas of soil conservation and human settlement in the parallel ridge valley of Yuzhong. ③ The input of farmland water conservation facilities was helpful in improving the coordination level, and reasonable control of the planting area could also more positively affect the coordination relationship between the soil and water conservation policy and agricultural ecological efficiency. The robustness of the regression results is confirmed using a counterfactual test. [Conclusion] To effectively maintain soil and water resources and agricultural ecological security, the Three Gorges reservoir area (Chongqing section) should adhere to the principles of local governance and regional linkages, actively guide all parties in society to participate in the formation of governance synergy, and jointly promote the development of a diversified support model combining poverty alleviation, soil conservation, and agricultural assistance.