Hillside buildings are particularly vulnerable to earthquakes owing to their structural configuration; however, research addressing this issue remains limited. This study investigates the effectiveness of high-damping rubber bearings (HDRBs) in enhancing the seismic resilience of hillside structures. Five numerical models were analyzed using non-linear time-history (NTH) analysis, including two flat-plane structures (one isolated and one with a fixed base) and three dropped-layer structures on hillside terrain (one with base isolation, one with inter-story isolation, and one with a fixed base). Deformation history integral (DHI) modeling was employed to simulate the HDRBs. Six earthquake ground motions from the PEER database and one scaled from 0.2–0.8 g were used to assess the seismic responses of the buildings. The results indicate that HDRBs significantly improved the seismic performance. The flat-plane isolated system (FIS) model achieved a nearly 90% reduction in peak roof acceleration compared to fixed-base structures. The dropped-layer isolated system (DIS) and dropped-layer inter-story isolated system (DIIS) models exhibited reductions of approximately 80% in the peak roof acceleration. Furthermore, the isolated structures demonstrated up to 78% reduction in the maximum inter-story drift, along with significant decreases in the story shear forces and overturning moments. Compared with non-isolated dropped-layer structures, the DIS and DIIS models showed reductions of 70% and 55% in the base shear force, respectively. The results highlight the efficacy of HDRBs in energy dissipation and their significant role in enhancing the seismic resilience of mountain structures.