This paper analyzes the current situation of cross-border e-commerce of fresh agricultural products in China regarding import and export trade, e-commerce development and logistics services, and summarizes the existing problems and influencing factors. Through the establishment of AHP-fuzzy comprehensive evaluation model, according to the established index system, the weight of each index factor is determined by using hierarchical analysis, and the importance degree of the influencing factors is calculated using fuzzy comprehensive evaluation method. The results show that among the primary indicators, the supply of fresh agricultural products has the highest influence, with a score of 4.49. Among the secondary indicators, the quality of new farm products and cross-border e-commerce trading platforms have a very high degree of influence, with scores of 4.714 and 4.518, respectively. The study provides a vital decision-making support for optimizing the development of cross-border e-commerce for fresh agricultural products.