Abstract: Rural express logistics distribution plays the role of bearing the “bearing up and down” in the urban and rural economic and social development, and its distribution mode affects its distribution benefits. However, the three typical rural express logistics distribution modes have certain problems. Guided by system science theory, this paper explores the“bottleneck”that restricts the development of rural express logistics distribution. From a macroscopic perspective, qualitative analysis is carried out on the factors that affect the mode of rural express logistics distribution. On this basis, the system dynamics modeling method is used to establish the rate variable fundamental in-tree model of the factors affecting the mode of rural express logistics distribution. The fundamental model analysis technology is used to analyze its operation mechanism and generate management countermeasures. Under the guidance of system development management strategies, it puts forward suggestions on developing the characteristic economy according to local conditions, improving the logistics infrastructure, and supporting the rural distribution development by multi-party cooperation.