The rapid development of e-commerce has a profound impact on agricultural supply chain finance (ASCF), which is of great significance to enhance the resilience of agricultural economic development, realize the poverty alleviation effect of agricultural enterprises, integrate agricultural supply chain resources and solve the financing difficulties of agricultural enterprises. We analyze the participants and functions of the ASCF mode based on e-commerce, and the contract framework of various participants when they operate in the ASCF platform in this paper. Based on the agricultural industry chain, we analyze the operation process of accounts receivable financing mode, inventory financing mode and prepayment financing mode based on E-commerce. Finally, in view of the natural risks, credit risks, logistics risks, technical risks and legal risks that may exist in ASCF based on e-commerce, the corresponding countermeasures are put forward from the aspects of dispersing natural risks, building digital credit risk assessment system, building agricultural logistics network system, improving technical risk monitoring system, and improving relevant laws and regulations policy recommendations.