Abstract: In recent years, the frequent occurrence of earthquakes has drawn increasing attention to the seismic safety of underground structures. As a critical passage connecting the ground surface and underground space, shafts have been widely used in urban underground space development and energy resource exploitation. Previous post-earthquake investigations indicate that shaft structures generally suffer severe seismic damage, such as lining cracking and water leakage, particularly at locations where they intersect rock–soil interfaces. However, the influence mechanisms of vertical ground motions on the dynamic response of shaft structures remain unclear. Therefore, this study takes a cast-in-place shaft as the research object and employs three-dimensional finite element dynamic time-history analysis to establish a soil–structure interaction model of a shaft crossing a rock–soil interface. The effects of different interface depths and stiffness contrasts between rock and soil on the internal forces and strain responses of the shaft under vertical seismic excitation are systematically investigated. The results show that the vertical seismic response of the shaft is significantly affected by both the interface depth and the stiffness contrast between rock and soil. With increasing interface depth, both the axial strain and circumferential strain at the interface increase, leading to an enhancement of the axial deformation of the shaft. Moreover, as the relative stiffness between rock and soil increases, the vertical strain of the surrounding soil increases, whereas the axial and circumferential strains of the shaft decrease.