In recent years, fresh agricultural products safety incidents emerge one after another, fresh agricultural products cold chain logistics risk has become the pain of the supply chain. This study firstly summarized the current situation of fresh agricultural products cold chain logistics and the research results of relevant literature, proposed the direction and purpose of this study, and then established a risk warning system for fresh agricultural products cold chain logistics risk. Through expert interviews, questionnaires and other ways to collect relevant data, combined with the characteristics of fresh agricultural products cold chain logistics sorted out based on operational risk, equipment risk, management risk, information risk and accident risk risk index system; Finally using SPSS21.0 for data analysis, through the establishment of the linear equation build up fresh agricultural products cold chain logistics risk early warning model, provide quantifiable results for fresh agricultural products enterprises, through the empirical analysis to verify the model feasibility, and further enrich the study of fresh agricultural products research, has certain practical significance and academic value.