Previous studies reached contrary conclusions regarding the train effect on the lateral structural vibration of track-bridge system. Existing shaking table tests failed to address the contrary due to their lack of running train model. In this paper, a shaking table test with a running train model was carried out to verify the train hitting and damping effects, and evaluate the effect degree of train operation on the structural vibration. The results show that the hitting effect on the track structure vibration is considerable but that on the bridge structure vibration is limited; the damping effect on the track and bridge structure vibrations is not significant; under seismic excitation, the irregularity-induced vibration increment of track structure reaches 300%, while that of bridge structure is small; the aseismic design of high-speed railway track-bridge system can be simplified by ignoring the train if the bridge structure response is adopted as the major evaluation index.