<p>Ancient masonry pagodas are highly vulnerable to earthquake damage because of their large slenderness ratio and low tensile strength. Existing seismic analyses usually simplify the foundation as a homogeneous medium and rarely consider the reflection and transmission of seismic waves at layered soil interfaces, which may lead to an inaccurate assessment of soil–structure interaction (SSI). To address this issue, this study investigates the Wenfeng Pagoda in Fenyang, China, with particular emphasis on the influence of wave propagation in the rammed earth foundation on its seismic response. Within the framework of the viscoelastic artificial boundary, an improved three-dimensional wave-input method is proposed. The method considers wave reflection and transmission at soil-layer interfaces and is implemented in Abaqus through equivalent nodal forces. Comparative models with rigid, homogeneous-soil, and layered rammed earth foundations are then established to analyze the dynamic characteristics, acceleration and displacement responses, and damage evolution of the pagoda. The results show that SSI significantly reduces the higher-order natural frequencies of the pagoda system, amplifies displacement and acceleration responses, and shifts seismic damage from the upper part toward the middle and lower sections. Compared with the homogeneous soil foundation model, the rammed earth foundation improves the overall system stiffness and mitigates structural damage. Moreover, the improved wave-input method further reduces the seismic response by capturing wave attenuation caused by reflection and transmission at layered interfaces. This study provides a theoretical basis and a refined numerical approach for the seismic analysis of ancient masonry pagodas.</p>