With the continuous development of the economy, there has been a significant improvement in residents’ living standards and consumption abilities. In addition, there is a growing awareness of health consciousness, leading to an increased demand for fresh food products. Fresh food supermarkets’ cold chain systems play a crucial role in ensuring the freshness of various products, preserving their nutrients, and minimizing losses during transportation. This, in turn, helps to reduce costs and increase profits. Therefore, it is imperative to establish a practical and effective risk identification system for the supply chain of fresh food products and continuously conduct research on the risks associated with these products. This study aims to analyze the current situation of cold chain logistics development in China, conduct a comprehensive analysis of the risks present in the supply chain of fresh food products, and utilize the Analytic Hierarchy Process (AHP) and Fuzzy Comprehensive Evaluation (FCE) methods to identify and evaluate the risk factors associated with fresh food products. The ultimate goal is to promote the development of cold chain logistics in China and expand the market for fresh food products.