A numerical framework was proposed for the seismic analysis of underground structures in layered ground under inclined P-SV waves. The free-field responses are first obtained using the stiffness matrix method based on plane-wave assumptions. Then, the domain reduction method was employed to reproduce the wavefield in the numerical model of the soil–structure system. The proposed numerical framework was verified by providing comparisons with analytical solutions for cases involving free-field responses of homogeneous ground, layered ground, and pressure-dependent heterogeneous ground, as well as for an example of a soil–structure interaction simulation. Compared with the viscous and viscous-spring boundary methods adopted in previous studies, the proposed framework exhibits the advantage of incorporating oblique incident waves in a nonlinear heterogeneous ground. Numerical results show that SV-waves are more destructive to underground structures than P-waves, and the responses of underground structures are significantly affected by the incident angles.