In this study, the Y-column subway station of the Xinhua Street Station in public areas of the Beijing Metro Line 6 was used as an engineering background to develop a numerical model with the FLAC^3D finite difference program. The model was used to analyze and research the seismic response characteristics of the large-span high-section Y-shaped column subway station under only ground horizontal vibrations as well as under a combination of both horizontal and vertical seismic waves. The results showed that compared with inputting only one-way seismic waves, the peak acceleration and stress value of the station increased and the relative horizontal displacement decreased under the two-way seismic coupling. When the strength of the seismic wave input increased, the impact rate of vertical ground motion showed a decreasing trend. Under the combined action of the two-way seismic waves, the vertical displacement of the Y-shaped column fork branch was significantly increased under the same conditions and the vertical displacement of the measuring point was more uniform, whereas the vertical displacement of the measuring point in the one-way horizontal motions was quite different. Compared with the one-way horizontal motion, the vertical seismic wave input was less affected by the horizontal-direction vibration characteristics law among each measuring point.