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. A tunnel project crossing a fault fracture zone in a high-seismic-intensity area of Southwest China was taken as the research object. By comprehensively analyzing the seismic dynamic response of water-bearing fault tunnels from multiple dimensions, including the time domain, frequency domain, and time-frequency domain, and by combining the strain evolution characteristics and failure phenomena of the tunnel, the seismic failure mechanism of water-bearing fault tunnels was revealed. The results show that under a 0.2g earthquake, the water-bearing fault significantly influences the acceleration response of each monitored tunnel section, The average increase of the dynamic amplification effect of in the intact surrounding rock area is greater than that in the water-bearing fault section. Fourier spectrum analysis after fault water injection 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 after fault water injection, the overall amplitude of the tunnel response is significantly reduced, and the spectral characteristics change from a single-peak distribution before water injection to a multi-peak distribution. After fault water injection, the stress state of different parts of the tunnel changes significantly; the crack development in the tunnel section passing through the water-bearing fault is more severe, mainly concentrated in the vault, arch waist, and arch bottom, while the damage of the tunnel in the intact surrounding rock section is concentrated on both sides of the arch bottom and the arch waist area. This research contributes to determining a rational seismic fortification design for practical engineering of tunnels crossing water-bearing faults and is of great significance for understanding the seismic dynamic response characteristics of such tunnels.