China's agricultural development is relatively backward, resulting in a serious lag in the development of agricultural product logistics, which not only greatly weakens the market competitiveness of China's agricultural products, but also has become the bottleneck of China's entire distribution system. Based on the current characteristics of agricultural product logistics in my country, this paper analyzes the impact of e-commerce on agricultural product logistics and puts forward the key points of the construction of agricultural product logistics system under e-commerce. This paper first describes the meaning of agricultural product supply chain logistics, and the seasonality of agricultural product supply chain logistics strong, large transportation volume and the composition of the supply chain logistics, transaction, and other cost systems, and then analyze based on the characteristics of the agricultural product supply chain and the composition of the cost system, and finally sort out some methods to adjust the logistics cost of the supply chain .