Underground rail transit is the lifeline of urban transportation. Due to the frequent occurrence of earthquakes and the increasing frequency of train entry and exit in China, the structure of subway stations is susceptible to both seismic and train loads. However, the current research on the seismic performance of subway station structures has not considered the practical problem of seismic and train load coupling. In order to ensure the safety of subway station structure when the seismic struck as the train was entering and leaving the station occur, a three-dimensional refined calculation model of soil, subway station and track interaction is established. The load form of train braking entering the station is selected to apply on the track surface, and the three-dimensional seismic wave is input at the bottom of the model. The variation law of stress, displacement and acceleration of subway station structure under the two working conditions of seismic action and seismic train coupling action is compared and analyzed. The results show that under the coupling effect of seismic and train, the peak stress at the bottom of the lower column is the highest, which is the weakest position of the station structure. After deformation occurs, the maximum yield stress value is first reached and plastic failure occurs. In the early stage of train arrival (0~5 s), the acceleration and displacement amplitudes of the board under seismic train coupling are greater than those under seismic action. In the later stage of train arrival, the acceleration and displacement of the board under both working conditions are basically the same. Under the coupling effect of seismic and train, when the seismic acceleration is small and the train speed is high, resonance occurs when the vibration frequencies of the two are close, leading to the amplification of the vibration of the plate.