Abstract: A finite element method-indirect boundary element method (FEM-IBEM) coupling method is proposed for nonlinear seismic response analysis of underground structures in water-saturated soft soils based on the Biot’s theory of a poroelastic medium. The FEM-IBEM coupling method can consider the dynamic coupling between solid frame and pore water, dynamic soil-structure interaction as well as soil nonlinearity through equivalently linear analysis. The particular advantage of the proposed coupling method is that the calculations of the FE subdomain and the IBE subdomain are independent as well as parallel. Thus, the soil nonlinearity of both the FE subdomain (near field) and the IBE subdomain (far field) can be considered by avoiding the interactive computation between them. The FEM-IBEM coupling method is validated by comparing with the results in the existing literatures. The seismic internal forces and deformations of a two-story subway station in water-saturated soft soils in Tianjin coastal district are studied. The differences in the seismic responses of the subway station between soil linearity and nonlinearity are compared, and those in the seismic responses of the subway station between water-saturated soils and dry soils (single-phase media) are also compared. It is shown that the soil nonlinearity and the dynamic coupling between solid frame and pore water significantly influence the seismic responses of the subway station including structural internal forces and deformations.