Abstract: Taking Shanghai soft soil site metro station structure as analysis object, through two typical stations of two-storey-three-span and three-storey-three-span, with site depth and bottom boundary type, 8 groups of site-station structure analysis model are composed. The station structure seismic response analysis difference is investigated. Reasonable method of choosing boundary range and type for metro station structure transverse seismic response analysis model is discussed. Results show that when viscoelastic bottom boundary is adopted, the responses of different depth models are basically the same. When fixed bottom boundary is used to simulate the rigid bedrock, the calculation results of the 70 m depth model are conservative, and the seismic response of the structure will be amplified by about 55%.