Regional extreme rainfall events have occurred frequently in China, and subway tunnel construction faces possible threats under extreme weather conditions. Thus, in this study, we used the set pair analysis (SPA) approach to the construction safety evaluation of subway tunnels and developed a construction safety evaluation model under extreme rainfall circumstances. Firstly, based on careful consideration of the complex construction environment of subway tunnels under extreme rainfall weather conditions, a construction safety evaluation system of subway tunnels was developed considering four aspects: rainfall, hydrogeology, construction design, and management. Moreover, the weighting analysis of each index factor was carried out using the improved analytic hierarchy process (IAHP) method, the entropy weight method (EWM), and the linear weighting method. Secondly, considering the uncertainty of subway tunnels’ construction safety evaluation system and the fuzzy nature of evaluation-level classification, a construction safety evaluation system of subway tunnels based on the multivariate linkage number and set pair analysis theory was established. Finally, we applied the model to a subway tunnel construction case. The results show that the evaluation results are consistent with the actual engineering survey results, which verifies the practicality and effectiveness of the model in evaluating subway tunnel safety. We also determined the primary factors and risk development trends that affect the safety of subway tunnel construction under extreme rainfall weather conditions to guide the safety risk management of subway tunnel construction.