This study proposes a ground-boundary scatter method for calculating wavefields in layered sites with stepped topographies. The total wavefield is decomposed into the free field of the flat site and the reflected wavefield from the ground. The wave-reflection equivalent forces are calculated through a dynamic analysis of the ground-boundary substructure intercepted from a full-domain site model. In the scattering analysis, a scaling-line-based scaled boundary finite-element method in the time domain is developed for the high-accuracy simulations of semi-infinity in an asymmetric layered half-space. A domain reduction method based on accurate wavefield solutions is used to analyze the soil–structure interaction. The proposed method makes complex topography-dependent wavefield calculations more flexible and practical, thus overcoming the limitations of traditional methods for seismic input. It can be used for localized arbitrarily shaped stepped topographies based on near-field finite-element models, thereby satisfying engineering requirements. The detailed implementation steps are described. For validation, numerical examples of wave propagation are for in homogeneous and layered stepped half-space containing valleys and irregular stepped terrains under different plane-wave incidence directions. The engineering applicability of this method is benchmarked through the seismic analyses of a nuclear structure built on different single-faced stepped-topography sites, revealing its potential adverse effects on structural response.