The nonlinearity of the ballastless track-simply supported girder bridge primarily manifests in the bearings and track structure during earthquakes. While existing research has elucidated the effects of bearing nonlinearity on running safety during earthquakes, the effects of track structure nonlinearity remain unclear. Therefore, this study further explores the effects of track structure nonlinearity on running safety during earthquakes. First, a dynamic analysis of the train-track-bridge coupled system (TTBCS) incorporating track structure nonlinearity, was performed using the ANSYS-TRBF (train-rail-bridge-foundation coupled system dynamic analysis software, TRBF) co-simulation approach to assess running safety during earthquakes. Then, by comparing results from the TTBCS models both with and without track structure nonlinearity, this study clarified the effects of track structure nonlinearity on dynamic response and running safety assessment (RSA) indices. It was found that neglecting track structure nonlinearity during earthquakes can result in an overestimation of the Nadal, leading to an inaccurate RSA. Moreover, this effect intensifies as the seismic intensity increases. By explaining these results, this study elucidates the mechanism by which track structure nonlinearity affects running safety. Finally, this study specified the necessary seismic intensities and vehicle speed ranges needed to consider track structure nonlinearity, and established a comprehensive influence domain. This study reveals the effects of track structure nonlinearity on running safety during earthquakes, contributing to a more accurate RSA during earthquakes.