For large-section tunnels crossing fault fracture zones, indoor experiments were conducted to study the mechanical and permeability characteristics of the rock specimen. Based on the correlation between rock integrity index and physical and mechanical indicators, the parameters of surrounding rock under different degrees of fragmentation were quantified. Considering the permeability of surrounding rock changes with confining pressure, a three-dimensional numerical model was established to analyze the impact of the engineering characteristics of fractured zone surrounding rock on the tunnel deformation. Through on-site monitoring, the deformation of the tunnel and the stress changes of the support structure are mastered. The results show that: (1) The mechanical properties of the rock specimen in the fractured zone are greatly affected by the water-rock interaction, and the peak stress of the rock specimen in the saturated state is significantly reduced compared to the dry state. (2) The permeability of the rock specimen in the fractured zone decreases in a logarithmic relationship with the increase of confining pressure. When the confining pressure exceeds the crack closure stress, the penetration water pressure of the rock sample approaches. (3) As the integrity index K_v of the rock mass in the fault fracture zone decreases, the maximum settlement of the tunnel arch increases in a logarithmic relationship, and the adverse effect of seepage on tunnel deformation increases. (4) By taking reasonable strengthening support measures and parameters, the tunnel can safely pass through the mileage section of the fault fracture zone, which can be used as a reference for engineering applications.