To explore the influence of shield construction on the stress of tunnels surrounding rock and linings in deep, high groundwater and low-permeability soft rock strata, a 3D coupled hydro-mechanical model of a low permeability mudstone tunnel was established with ABAQUS, based on the effective stress principle and the Mohr–Coulomb elastoplastic constitutive model, taking the Bailuyuan Tunnel of the Hanjiang to Weihe River Valley Water Diversion Project Phase II in China as an example. The tunnel shield construction was simulated, and the spatial-temporal variation in the pore water pressure and the internal forces of the lining were studied. The results show that the central pore water pressure of the low-permeability mudstone face presents a V-shaped variation with the tunnel excavation. When the face was approximately 15 m from the representative section, the pore pressure on the linings basically varied between 192.7 and 182.5 m. The bending moment and axial force of the lining increased by 7.4% and 12.8%, respectively, with shield tunnelling. When the tunnel diameter was constant, the axial force and bending moment of the lining decreased quadratically as the lining thickness increased. The influence of shield construction decreased as the lining thickness increased. The research results provide a reference for the safe and optimal construction of the Hanjiang to Weihe River Valley Water Diversion Project.