To investigate the effect of fluid -solid coupling on the seismic performance of underground structures in watersaturated soil, a comparison study is conducted in this paper on three-dimensional (3D) nonlinear seismic behavior of a 3 -story 3 -bay subway station obtained using two different finite element methods (FEM), i.e., the generally used simplified method with equivalent single-phase soil model and a newly developed 3D numerical approach capable of considering the dynamic behavior of saturated two-phase media. A 3D user -defined element embedded in ABAQUS is first introduced to simulate saturated soil's dynamic fluid -solid coupling effect. Then, more essential demonstrations are presented for establishing and validating the two FEM. Based on the two methods with and without incorporating fluid -solid interaction, 3D nonlinear seismic response analysis is performed on the subway station considering three different input seismic waves. Discussions are conducted in terms of accelerations, lateral displacements, inter -story drift ratios, rotation of columns, damage characteristics, and internal forces, based on which the limitations of the simplified method are quantitatively interpreted. The results show that neglecting the fluid -solid coupling effect can bring about conservative evaluations of the seismic behavior of underground structures in saturated soil. The effect of fluid -solid coupling on the seismic performance of underground structures is quite sensitive to the peak ground acceleration. It is significant to consider the fluid -solid coupling effect during the performance -based seismic design of underground structures enclosed in saturated soil to gain realistic seismic responses, especially for those subjected to major earthquakes.