Abstract: The Three Gorges Reservoir Area is a key control region of eco-environmental construction in China. However, how to achieve agro-economic development and control agricultural non-point source pollution in the region have emerged as difficult issues in recent years. To verify the coupling process of agricultural eco-economic system under emission mitigation and sink enhancement, data from the Zhong County (a typical non-point source pollution control district in the Three Gorges Reservoir Area) was used to develop eco-agriculture and non-point source pollution control. Then an equation-driven model of the construction structure was studied in terms of the interrelationship and interaction paths of the various elements of agricultural resources, agricultural development and agricultrual eco-economic coupling system in the Three Gorges Reservoir Aarea of Zhong County under the backdrop of emission mitigation and sink enhancement of non-point source pollution policies and measures. The paper put forward 6 basic assumptions based on 4 latent variables (emission mitigation and sink enhancement of non-point source pollution policies and measures, agricultural resources, agricultural development and coupling degree of agricultural eco-economic system) and the corresponding observation variables. Based on these elements, the paper designed a coupling model of the agricultural eco-economic system. The empirical results revealed that the path coefficient of the interrelationship between agricultural non-point source pollution control measures and agricultural resources utilization was 0.79. This suggested that the government's emission mitigation and sink enhancement measures promoted rational utilization of agricultural resources in the region. The path coefficient of the interactive relationship between emission mitigation and sink enhancement measures of agricultrual non-point source pollution and agricultural development was 0.80. This also suggested that the measures and policies were strong incentive for agricultural development in the study area. The path coefficient of the relationship between agricultural development and resources utilization was 0.77, indicating that agro-economic development in the region was based on reasonable agricultural resources utilization. Emission mitigation and sink enhancement measures positively influenced the coupling process of agricultural eco-economic system. The path coefficient was 0.85, which suggested that the measures in the study area significantly improved the coupling process. The utilization of agricultural resources and development positively influenced the process of agricultural eco-economic system coupling. The respective path coefficients were 0.91 and 0.89, indicating that the coupling process of agro-industry and agro-resources system conformed to the nature of agricultural development. Considering the structural relationship between the latent variables, it was noted that under background of non-point source pollution emmission mitigation and sink enhancement measures, agriculturla resources and economic development were the key elements of system coupling. The elements formed an effective perspective for understanding the coupling process of the system.