The Hexi Corridor and northern Qilian region, adjacent to the Beishan underground research laboratory (URL) for the geological disposal of high-level radioactive waste, exhibit complex seismic environments characterized by frequent strong earthquakes. The Beishan URL, featuring a complex underground structure consisting of three vertical shafts and a spiral ramp, displays significant large-scale spatial distribution characteristics. Investigating the seismic response characteristics of the underground structure group holds great engineering significance for the subsequent assessment of crustal stability at the site. Based on the design of the URL, along with existing physical and mechanical parameters of surrounding rocks, this study established a fine-scale three-dimensional finite element model of the rock mass-underground structure system. Using this model, this study investigated the impacts of key faults on the near-field seismic safety of the URL. The results indicate that traditional seismic attenuation relationships are difficult to consider near-source effects, such as finite fault effects, fracturing directivity effects, and hanging wall effects. In contrast, the stochastic finite-fault method can effectively consider these near-field ground shaking characteristics. The target site exhibits hard granite bedrock, and the response spectra of the earthquakes induced by near-field seismogenic faults, received at the site, display pronounced high-frequency components. Furthermore, the ground shaking of the underground cavern group, caused by the irregular structure of the URL, presents significant spatial variability, with the rock mass softening zone exhibiting a notable accumulation of peak ground acceleration. This zone should be avoided in engineering applications. This study offers a basis for seismic safety analysis for the future site selection and evaluation of the disposal repositories of high-level radioactive waste.