Abstract: In recent years, earthquake damage cases have shown that underground structures are subjected to the threaten of earthquake motion. Scholars have carried out a lot of research on the seismic response of underground structures. Because vertical shafts are functionally connected to the surface and underground space, it is inevitable to face the problem of crossing the rock-soil interface, and there is a relative lack of research on the influence of the rock-soil interface on the seismic response of the shaft. The dynamic response of the shaft structure passing through the rock-soil interface stratum environment is unclear. Therefore, this paper mainly studies the influence of the position of the rock-soil interface and the relative stiffness between rock and soil on the seismic response of the shaft. Based on the finite element analysis software ABAQUS, a three-dimensional soil-structure interaction model between the site of rock-soil interface and shaft is established. The dynamic time-history analysis method of equivalent linearization is used to study and analyze the internal force change and deformation of shaft under horizontal ground motion. The results show that the sudden change of the internal force happened at the rock-soil interface, and greater axial force and bending moment at deeper position lead to larger strain and diameter deformation rate. When the relative stiffness of rock and soil is larger, the internal force and deformation of the shaft at the rock-soil interface are larger than those with smaller relative stiffness. In the engineering design, enough attention should be paid to the shaft structure crossing the rock-soil interface.