With the rapid development of rail transportation, environmental issues of subway become more and more significant, while the thermal comfort of passengers also draws wide attention. There are various arrival conditions for actual subway trains, and their effects on subway stations and passengers have rarely been studied. This paper is the first to investigate the piston effect of subway trains under single and double train arrival conditions and its impact on passenger thermal comfort. Firstly, a transient 3D numerical model based on the real metro station is established. Then, the influencing factors of the piston effect are analyzed, including the maximum travel speed of single train and the different arrival time intervals of two trains. Moreover, inhomogeneity coefficient (Kt and Ku) and the predicted mean vote (PMV) model and the predicted percentage dissatisfaction (PPD) index are introduced to analyze the thermal comfort. The results show that the two-train condition has a more uniform temperature and velocity distribution than the single-train condition. However, the best thermal comfort is obtained for the two arrival conditions of single train traveling at 16.2 m/s and two-train arrival time interval of 1s from the PMV and PPD. Besides, the fresh air volume of the two-train model is increased by 100% than that of the single-train model, which indicates that the double-train model is better than the single-train for station ventilation. These studies provide important theoretical guidance and references for optimizing metro train operation strategies and the design of thermal environments in metro stations.