Recently, subsea tunnel construction has developed rapidly in China. The traffic volume of subsea metro tunnels is large. Once a safety accident occurs, economic losses and social impacts will be extremely serious. To eliminate accidents in operational subsea metro tunnel structures, a health risk prediction method is proposed based on a discrete Bayesian network. Detecting and monitoring data of the tunnel structures in operation were used to evaluate the health risk by employing the proposed method. This method establishes a Bayesian network model for the health risk prediction of the shield tunnel structure through the dependency relationship between the health risk of the operational tunnel structure and 13 risk factors in five aspects: the mechanical condition, material performance, integrity state, environmental state, and deformation state. By utilizing actual detection and monitoring data of various risk factors for the health risk of the operational subsea metro shield tunnel structure, this method reflects the actual state of the tunnel structure and improves the accuracy of health risk predictions. The validity of the proposed method is verified through expert knowledge and the subsea shield tunnel structure of the Dalian Subway Line 5. The results demonstrate that the health risk prediction outcomes effectively reflect the actual service state of the shield tunnel structure, thus providing decision support for the control of health risks in the subsea metro shield tunnel.