With the extension of high-speed railways to high-intensity earthquake regions, it is impossible to avoid structural vibrations due to the joint action of trains and earthquakes. Therefore, it is of great significance to study the influence trains on bridge structures exposed to earthquakes. In this paper, a coupled finite element analysis model of a high-speed railway vehicle-bridge was established by considering a simply-supported beam bridge with the China Railway Track System (CRTS) II plate and the CRH2C high-speed train. The correctness of the model was experimentally verified. By considering the ground motion randomness, the influence of the train on the response of the bridge structure exposed to an earthquake was analyzed. Also, the influence level of the running train on the seismic response of bridge structures with different pier heights was studied. The results revealed that the train dynamic effect significantly reduced seismic responses of piers and supports, and that the effect itself decreased with the pier height increase. Furthermore, the dynamic effect of the train increased the seismic response of the track structure, while the bridge pier height had little influence on the dynamic efficiency of the track structure. For different pier heights, the probability distribution model of the train dynamic effect for the track-bridge system seismic response was considered as the normal distribution. This indicated that the seismic response of the track-bridge system under vehicle condition could be simplified as the product of the seismic response and safety factor under no vehicle condition.