By borrowing ideas from the reliability analysis in reliability engineering theory, the abstract problem of coldchain logistics system fault is crystallized and its fault tree is constructed according to operation features of various functional parts and the causal relationship between events in cold-chain logistics system. By converting fault tree to Bayesian networks, it is convenient to draw a comprehensive evaluation for the system reliability of cold-chain logistics system and reveal the main cause of system failure, in order to provide quantitative foundation for improving system reliability. In a third party cold-chain logistics enterprise, expected results are obtained by applying the proposed method.