The problem of crossing active faults is inevitable during the construction of water diversion power stations or long-distance water conveyance projects, therefore it is critical for the engineering sector to adopt particular lining structure in hydraulic tunnels to traverse active faults. Based on the actual situation of a certain hydro project, the feasibility and rationality of the multi-layer flexible composite lining structure are discussed by the finite element numerical analysis. In addition, the influences of fault displacement, fault width, fault strike and section length on the stress and deformation of the lining structure are analyzed. The calculation results show that: With the increase in the fault displacement, both the deformation and stress of the steel lining present an increasing trend. However, due to the setting of the expansion joint, the stress of the steel lining is marginally affected by the fault displacement. The smaller the angle between the pipeline and the fault strike, the greater influence on the stress and deformation of the steel lining structure. When the pipeline is orthogonal to the fault, the stress condition of the steel liner is optimal. While the stress condition of the steel liner becomes worse, as each expansion joint bears more fault displacement due to larger length of the steel pipe section or the fewer number of expansion joints. The research results of this paper can provide a reference for the structural design of high-pressure water conveyance tunnels when dealing with the creep deformation of faults.