This paper investigates the seismic properties of a cross transfer subway station under a horizontal earthquake wave in soft soil stratum. A 3-D simulation analysis model is established considering the dimensions and soil layers of a real structure. The HS-small model is employed to simulate the non-linear stiffness of soft soil. The dynamic responses of a single station case and a cross transfer station case are explored, followed by the direction of the input earthquake wave, the type of soil reinforcement in the overlapping area, had on the dynamic response were also analyzed. The simulation results show that the subway station has better seismic response than the single station, and soil reinforcement can increase the dynamic response of the different components in the overlapping area. As soil reinforcement stiffness increases, the dynamic response increases in both the upper and bottom stations at varying degrees. The findings from this paper provide a reference to the seismic design of cross transfer stations in similar ground.