Considering the effect of dynamic interaction between liquefiable soil and underground structure, simulating the nonlinear seismic response of underground structures through simple, convenient, and reliable 3D numerical model is still a great challenge at present. A three-dimensional numerical simulation method for dynamic response of underground structure in liquefiable site is proposed based on the centrifuge shaking table test designed for a subway station buried in liquefiable interlayer site carried out in the previous period. The numerical model takes into account the characteristics of sand prone to large deformation after liquefaction and the nonlinear characteristics of the contact between saturated soil and structure. The typical numerical calculation results are compared with the experimental results to verify the correctness of the numerical model, and the extended analysis of the structural damage is carried out, which visually shows the damage distribution of structure under different functional states after earthquake. The analysis of structural damage shows that the junction position of middle column and longitudinal beam is more prone to tensile damage under the horizontal earthquake action; while after considering the horizontal-vertical seismic effect, the middle column will produce additional compressive damage due to the vertical inertia force, and the end of middle column should be paid attention to in seismic design.