The application of shield docking method in soft clay can greatly shorten the construction period of long tunnels, but the excess pore water pressure generated by the first and second shield construction in the shield docking section can affect the soil stress state and formation stability. The fluid-structure coupling model for the shield docking method is established in soft clay. In terms of time, the time distribution of excess pore water pressure at different distances on the shield docking cross-section is analyzed. In terms of space, the longitudinal distribution of excess pore water pressure and the cross-sectional distribution of excess pore water pressure caused by the first and second shield construction are analyzed. In addition, the disturbance law of pore water pressure caused by shield docking construction is analyzed, and the construction parameters are analyzed. The analysis results show that when the shield docking is completed, the disturbance range of shield construction on the top of the arch is the largest, followed by the sides, and the bottom is the smallest. The influence range of excess pore water pressure generated by shield construction in front of the excavation face is 1.5 times that generated by the first shield construction, and its value is approximately 3.4 times the tunnel diameter. When the permeability difference of layered soil is too large, a sudden change in excess pore water pressure will occur. During the shield docking process, the disturbance caused by the first shield construction stage is significantly greater than that caused by the second shield, and the pore pressure disturbance index of the first shield to the arch is about twice that of the second shield at the docking position. When no grouting reinforcement is carried out at the docking position, it is recommended to reduce the supporting force of the tunnel face to 0.8 times the standard supporting force 2D (D represents the outer diameter of the tunnel) away from the docking position for both the first and second shields, or to perform advance grouting reinforcement before the first shield reaches the docking position, in order to reduce the disturbance during the shield docking process.