In order to further explore the rural ecological environment promoting the new retail format, the research on improving the mechanism of bilateral economic interest linkage between agricultural enterprises and farmers under the rural ecological environment promoting the new retail format was proposed. Through in-depth analysis of the bilateral interest linkage mechanism between agricultural enterprises and farmers under the new retail format, this study starts with specific cases to deeply summarize the specific problems of the bilateral economic interest linkage mechanism between agricultural enterprises and farmers under the development trend of the rural ecological environment and fully reveal the unreasonable phenomena in the linkage mechanism. The results show that the main problems of the current agricultural enterprise linkage mechanism are the frequent occurrence of default events, the low stability of the linkage, the loose connections, and the lack of risk sharing and value creation mechanisms. On this basis, starting from the economic benefits acquisition and development needs of farmers and enterprises, this paper focuses on the innovation and improvement strategies of the bilateral economic benefit linkage mechanism from the aspects of the development of cooperative economic organizations, capital investment, and innovation of the industrial operation mode.