E-commerce of agricultural products has developed rapidly in recent years, which has become an important part of agricultural products circulation system. However, the overall market penetration rate of the e-commerce of agricultural products is not high. Consumers’ trust and apperceived experience still need to be improved, and many e-business enterprises are in a state of deficit. The improvement of the traditional business mode focusing on products cannot effectively solve the current problems. With the new consumption trend, it is necessary to take service as the core to innovate the e-commerce supply chain of agricultural products. Therefore, the paper discusses the innovation of agricultural products e-commerce supply chain under the service-oriented logic. The results show that the e-commerce supply chain of agricultural products should be changed from the orientation of products to service based on the innovative updating of the service concept. Under the service-oriented logic, the core elements of agricultural e-commerce supply chain include emphasizing the process and experience, customer participation, value creation, and service orientation. It consists of three levels: innovation based on integrated solutions, innovation based on service scenarios and innovation based on service ecosystem.