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Aiming at the limitations of traditional reliability analysis methods in the evaluation of multi-state complex system, a reliability analysis method for multi-state system based on Bayesian networks is proposed. In this model the multi-state variable nodes of Bayesian networks are applied to represent multi-states of failure modes, the conditional probability tables and directed arcs are used to represent uncertain cause–effect relationships among the variables. Through bidirectional inference calculation of the priori and posteriori probability, the interrelationship between notes is obtained in order to identify the system weakness, and provide basis to improve system reliability. The proposed method is verified in reliability analysis of the cell production line, and the system reliability is effectively improved.