In view of the special needs of the development of agricultural supply chain finance, a scheme based on system dynamics analysis and optimization of agricultural supply chain finance is proposed. By the theory of system dynamics, the agricultural financial supply chain system according to the actual situation are is designed first. Then, based on the main operation modes of agricultural supply chain finance, the causal analysis diagram and the logical equation of system dynamics are provided. By logical reasoning on the supply chain and its members, the potential risks and bottlenecks of various influencing factors are identified. According to the simulation results and the statistical analysis of a large number of curves and related data, the case analysis summarizes the key factors affecting the coordinated operation of agricultural supply financial system, and provides corresponding countermeasures. Therefore, it is proved that all errors of the system dynamics model are within the allowable range, and the accuracy of the model is high, which meets the requirements of empirical analysis.