Abstract: The surface of natural sites is typically irregularly undulating, and the truncated side boundaries of the foundation present a stepped geometric profile due to elevation differences, rendering the direct calculation of the free-field wave motion difficult. Therefore, the seismic input can only be constructed based on approximate site wavefield characteristics. To enhance the accuracy of simulating topographic effects in soil-structure interaction analysis, this study decomposes the equivalent wave field at the truncated site boundary into a regular-site free field and an irregular-topography scattered field. Boundary elements along the ground surface are extracted to construct a topographic boundary substructure for calculating the equivalent scattering forces. Following this, the scattered and free-field motions are superimposed and mapped to the boundary nodes of the three-dimensional near field. Consequently, equivalent seismic forces incorporating topographic effects are obtained, offering robust seismic inputs for full-domain wave propagation simulations. By comparison with benchmark solutions, the accuracy and applicability of the proposed method in complex two- and three-dimensional wavefield problems are verified via wave propagation simulations involving irregular topographies over homogeneous or layered half-spaces. Furthermore, the method is applied to seismic analysis of nuclear structures in undulating sites. It is demonstrated that structural seismic responses are substantially underestimated by flat-site simplifications. Under large-scale topographic irregularities, the approximations inherent in seismic input methods significantly impact the structural dynamic responses. The proposed method expands the available computational approaches for full-domain wave propagation simulation of structure–undulating site systems.