Abstract: To investigate the dynamic response characteristics of surrounding rock in tunnels crossing water-bearing faults, a large-scale shaking table model test was conducted, taking a tunnel project crossing a fault fracture zone in a high-seismic-intensity area of Southwest China as the research object. By comprehensively analyzing the seismic dynamic response of the water-bearing fault tunnel from multiple dimensions, including the time domain, frequency domain, and time-frequency domain, and by combining its strain evolution characteristics and failure phenomena, the seismic failure mechanism of this tunnel was revealed. The results show that under a 0.2 g earthquake, the water-bearing fault significantly influences the acceleration response at various monitoring sections of the tunnel. The average increase in the dynamic amplification effect in the intact surrounding rock area is greater than that in the water-bearing fault section. Fourier spectrum analysis after water injection into the fault indicates that the amplitude variation trends of the vault, arch waist, and arch bottom of each tunnel section are basically consistent, while the amplitudes in the high-frequency band all increase to varying degrees. HHT time-frequency analysis shows that the spectral characteristics of the tunnel change from a single-peak distribution before water injection to a multi-peak distribution after water injection. Besides, the stress state of different parts of the tunnel changes considerably. Crack development in the tunnel section passing through the water-bearing fault is more severe, mainly concentrated in the vault, arch waist, and both sides of the arch bottom, while the damage of the tunnel in the intact surrounding rock section is concentrated in the arch bottom and the arch waist areas. The above research can supply a reference basis for the seismic design of tunnels crossing water-bearing faults, and bears great significance for revealing the seismic dynamic response characteristics of such tunnels.