Abstract: Wave reflection and transmission phenomena occur when seismic ground motion propagates to the soil-structure interface, and the surrounding soil is under three-dimensional (3D) cyclic shearing with reciprocating change of shear stress and normal stress difference. The 3D equivalent shear strain algorithm and the loading-unloading criterion are used to extend the 1D Davidenkov hysteretic model in association with an incremental excess pore water pressure (EPWP) model to the 3D stress state. A weakly coupled effective stress method in 3D stress state is established considering the coupling between the cyclic degradation of soil stiffness and the EPWP generation during cyclic loading. Based on the ABAQUS explicit solver, the proposed method is implemented, allowing to perform nonlinear seismic response analysis of soil-structure interactions in 3D liquefiable site. The numerical simulation is carried out against a shaking table test on the subway station in liquefiable site. The results show that the EPWP generation leads to the degradation of soil stiffness, which significantly affects the dynamic soil-structure interactions. The energy-focusing time at the soil-structure interface obtained by numerical simulation and the corresponding instantaneous predominant frequency are in good agreement with the test results. The proposed effective stress method can capture the dynamic soil-structure interaction characteristics in the shaking table tests. However, the effective stress level at soil skeleton significantly affects the EPWP generation. The incomplete density similarity ratio design of the shaking table tests can cause the distribution of the EPWP ratio in the model soil deviated with the prototype.