<p>Underground structures in near-fault regions are often subjected to strong vertical shaking, and the vertical peak ground acceleration may significantly exceed the value assumed in conventional seismic design. This study focuses on a metro station located in cobble and strongly weathered sandstone composite strata. A 3D nonlinear dynamic model is developed to investigate the structural dynamic response, soil–structure contact behavior, internal force response of the central column, and damage distribution under different vertical-to-horizontal peak ground acceleration ratios (V/H). The influence of burial depth on seismic response is also examined. The results show that the soil–structure system amplifies both the horizontal and vertical components of the input motion under near-fault ground motions, with the vertical amplification being more pronounced. Compared with non-pulse-like records, the Chi-Chi ground motion with velocity pulses produces larger vertical acceleration responses and vertical deformations. Strong vertical ground motion increases the normal contact pressure at the roof slab–soil interface and the axial force at the column ends, while also indirectly affecting the sidewall interface contact pressure and the shear force and bending moment responses at the column ends. Compressive damage is mainly concentrated at the base slab–sidewall corners, the base slab–central column joints, and the bases of the central columns. Increasing burial depth intensifies and expands the damage in these vulnerable regions, whereas stronger vertical ground motion primarily exacerbates local damage at the central column base and its adjacent joints, with the effect becoming particularly pronounced at V/H = 1.5. These findings provide a useful reference for the seismic design of underground structures in near-fault regions.</p>