This paper establishes a novel full-process numerical simulation framework for analyzing the 3D seismic response of mountain tunnels induced by active faults. The framework employs a two-step approach to achieve wavefield transmission through equivalent seismic load: first, a highly efficient and accurate FMIBEM (Fast multipole indirect boundary element method) is used for large-scale 3D numerical simulations at the regional scale to generate broadband ground motions (1-5 Hz) for specific sites; subsequently, using the FEM (Finite element method), a refined simulation of the plastic deformation of surrounding rock and the elastoplastic behavior of the tunnel structure was conducted at the engineering scale. The accuracy of the framework has been validated. To further demonstrate its effectiveness, the framework is applied to analyze the impact of different fault movement mechanisms on the damage to mountain tunnels based on a scenario earthquake (Mw 6.7). By introducing tunnel structure damage classification and corresponding damage indicators, the structural damage levels of tunnels subjected to active fault movements are quantitatively evaluated. The findings demonstrate that the framework successfully simulates the entire process, from fault rupture and terrain amplification to the seismic response of tunnel structures. Furthermore, the severity of tunnel damage caused by different fault types is ranked as follows: reverse fault > normal fault > strike-slip fault.