Abstract Bearing effects have not been deeply investigated in the dynamic analysis of a train–bridge coupled system subjected to earthquake motions, and existing studies on base isolation of railway bridges have typically not considered the running train. To fill these gaps, this paper develops the numerical model of a three‐dimensional train–wheel–bridge–bearing (TWBB) system for seismic analysis. The substructuring method is implemented to separate the TWBB system into the train, wheel–rail, bridge and bearing subsystems, and couple them using state‐space representations. The complete model of the TWBB system has three main features: fewer degrees of freedom (DOF) than traditional finite element methods, applicability to different types of bearings, and simplicity as no iterations in the simulation are required. Therefore, the proposed procedure demonstrates that the TWBB model is an efficient and flexible representation to obtain and predict realistic demands for engineering purposes.