Underwater docking construction by mine and shield method is a key technical issue in the construction of subsea tunnels, and understanding the seepage-stress coupling characteristics is the premise of safe construction and operation of the docking section of tunnels. This study employed a finite element software to carry out three-dimensional numerical simulation of on-site docking construction scheme. Based on the simulation results, the seepage characteristics, displacement deformation and stress change rules of different construction sections of the tunnel were analyzed, which revealed the seepage-stress coupling mechanism of the construction of the tunnel mine-shield docking section on the surrounding rock disturbance. The results show that after tunnel excavation, the pore water in the surrounding rock pools and continuously recharges to the tunnel cave perimeter and the excavation surface, resulting in a reduction of pore water pressure, the formation of precipitation funnels, an increase in the seepage rate around the tunnel cave perimeter, and a large amount of water influx during the excavation stage. Affected by the hydraulic gradient, the pore water pressure at the bottom of the arch is the largest, but setting up drainage measures can lead and drain the pressure during construction. During tunnel excavation, displacement deformation increases abruptly, and due to the influence of dewatering and pressure relief at the excavation face, vertical settlement occurs at the crown of the tunnel section before excavation. Compared with the shield method, the disturbance degree of the mine method construction is greater, and the distribution of principal stresses in the excavation sections using the mine method are consistent in different construction sections. The study can provide a reference for the safety evaluation of the underwater docking projects by mine and shield method in subsea tunnels.