Random analysis has emerged as the dominant approach for analyzing train-bridge coupled (TBC) systems, replacing deterministic analysis. This shift is driven by considerations of system economy and randomness. However, the seismic train running safety assessment with multiple non-Gaussian distribution parameters faces the double dilemma of low computational efficiency and inaccuracy for TBC systems. In this study, an approach is applied by the combination of the new point estimate method and moment expansion approximation (NPEM-MEA) to address this problem. Furthermore, the application of this approach is illustrated by the random dynamic responses of a three-dimensional TBC system subjected to random near-fault ground motions. Validation of the NPEM-MEA’s feasibility is conducted using the Monte Carlo method, and comparative analysis confirms the accuracy and efficiency of the method. Additionally, the influences of random near-fault ground motions are discussed based on the random dynamic responses and train running safety indices in the TBC system. The simulation results underscore the necessity of simultaneously considering the randomness of multiple parameters in seismic train running safety assessment. This methodology holds potential for safety assessments involving non-Gaussian random processes in complex systems of a similar nature.