Logistics is very important for the development of electronic commerce of fresh agricultural products. Service innovation can improve the logistics efficiency and the quality of logistics service for fresh product e-suppliers, and then enhance its’ competitive advantage and the ability of customers value creation. From two aspects of service innovation model and the mechanism of value creation, the paper analyzes the innovation of logistics service of fresh product e-commerce. The results show that four models of logistics service innovation can be adopted by fresh product e-suppliers, including logistics technology innovation, logistics concept innovation, logistics organization innovation, logistics service interface innovation, and also its’ different combinations. The mechanism of value creation from logistics service innovation is as follows: reducing the logistics cost, improving the quality of logistics service, and providing new logistics services, and then upgrading the logistics service capacity. Consumers can get better consumption experience with added value from quality logistics service.