A Mw 6.6 earthquake struck Luding county, in Sichuan province of China on 5 September 2022, causing severe damage of nearby infrastructures. The earthquake indicates an awakening of southeast branch of Xianshuihe fault since the last 1973 Mw 7.6 Luhuo earthquake in Sichuan, thus attracting attention from the public. A physics-based method, combining Spectral Element Method (SEM) and Finite Element Method (FEM), was presented in this paper to investigate the correlation between near-fault motions and response of a road tunnel, which has a closest distance of about 6.0 km to the fault. This method allows to incorporate the rupture details, geological irregularity, 3D velocity structure, as well as the underground tunnel. The ground motions simulated by SEM were validated by comparison to specific station records and empirical Ground Motion Model (GMM), which were subsequently input into the tunnel to obtain its axial deformation and sectional inner forces. Parametric study on tunnel alignment was conducted, and wavelet transformation was used to extract dynamic pulses from the ground motions. Results show that the tunnel response is remarkably affected by dynamic pulse directivity, and the axial forces could be dominated by permanent fault displacement for tunnel of the strike-normal alignment.