This paper selected representative soft site along the subway lines and created two-dimensional overall finite element analysis model about nonlinear dynamic interaction among soil, underground subway station, and ground structure based on Nanjing underground subway station. It explored the seismic response influence of neighboring high-rise structure on the two-layer and three-span island-type underground subway stations. The results showed that the structure near the subway station had a significant constraint effect on the deformation of subway station which is oriented to the structure, and the influence of deformation of subway station which is backward to the structure is related to vibration characteristics of the soil-underground structure interaction system. The influence of neighboring ground structure on the strain stress response of subway station is useful in most part of important nodes. However, this influence is disadvantageous in the outer part of connections of side walls and plates and middle plate-interior column connections.