When a tunnel is near a water-rich fault fracture zone, water and mud inrush disaster easily occurs, where the determination of the minimum safe thickness of water-resistant rock mass is a key issue. Based on the silo theory and the limit equilibrium method, models of water inrush in fault fracture zone were established under the conditions that the tunnel axis is orthogonal and parallel to the tunnel face respectively. The analytic formulas of the water-resistant rock mass influenced by ground stress were obtained. Then, the criterion of water inrush in fault fracture zone was established, and the influence of the width of the fault fracture zone on the minimum safe thickness of the water-resistant rock mass was analyzed. Finally, the research result was applied to the Yonglian tunnel and the Qilianshan tunnel. Results showed that the width of the fault fracture zone had a significant influence on the determination of the minimum safe thickness of the water-resistant rock mass when the width of the fault fracture zone was less than 200 m. The minimum safe thickness of the water-resistant rock mass of Yonglian tunnel was calculated as 7.34 m. Water inrush occurred in Yonglian tunnel due to the insufficient safe thickness. The minimum safe thickness of the water-resistant rock mass value of F6 and F7 faults in Qilianshan tunnel were 10.22 and 11.59 m respectively. In the construction of Qilianshan tunnel, it is safe to pass F6 and F7 faults with 12 m water-resistant rock mass, which indicates that the theoretically calculated value is relatively close to the actual value and has certain reliability.