Abstract: Crossing active faults is a difficult problem to avoid when building long-distance water transmission tunnels, and the structural form of pressure tunnels crossing active faults has not been thoroughly studied. In this study, a multi-layer flexible stacked lining suitable for pressure water transmission tunnels crossing active faults is proposed aiming at addressing the problems of the common anti-fracture measures for the tunnels crossing active faults as well as their characteristics. Based on the actual situation of a project, the finite unit method is used to analyze the stress and deformation of the structures under the condition of using different tunnel lining structures in the project. According to the calculated results, the reasonableness of the multi-layer flexible stacked lining structures is confirmed. The numerical simulation is used to assess the impact of cushion thickness and elastic modulus on the internal force response and fracture resistance of the tunnel structures. The findings demonstrate that the thicker the cushion thickness the larger the total deformation of the expansion joints. It is more favorable for the tunnel lining to adapt to fault dislocation. However, when the cushion thickness increases further, there is a certain adverse effect on the force of the lining, so it is recommended to choose the appropriate thickness of the cushion layer according to the amount of fault dislocation. It is not necessary to use a too-thick cushion layer. The change of elastic modulus of cushion has a significant effect on the stress of steel pipes. Considering the stress of steel lining, the damage of concrete and the adaptability to fault dislocation, it is recommended that the elastic modulus of the cushion be selected as 3 to 5 MPa. The research results can provide some references for the design of pressure water transmission tunnels crossing fault zones.