Relying on the Mawan undersea large-diameter, dual-line, mud–water-balanced shield tunnel project and focusing on the characteristics of the tunnel, such as the complex geological conditions at the expected intersection location and the existence of a superimposed perturbation or secondary perturbation effect, theoretical calculations and three-dimensional numerical simulations were used to reveal the ground disturbance situation of the large-diameter, two-lane mud–water shield when it is propelled under various working conditions. The working conditions were set for the dynamic intersection of the left and right lines, with stopping and moving as the two modes, and a traversing simulation was carried out under three conditions related to the strata. The results show that the surface settlement curve for the two-lane construction became a “W”-shaped bimodal curve due to the superposition effect; the dynamic intersection construction greatly disturbed the ground layer and there was a plastic zone expanding outward at a small angle above the tunnel, with shear damage in the soil layer and tensile damage in the rock layer. A “one line stops, and another advances” intersection can reduce the impact of disturbance; the surface settlement value after the completion of the advancement was smaller than the dual-line intersection. The surrounding rock stress and displacement under the advancement of a single shield machine did not change to a great degree, there was no obvious change in the surface settlement above the tunnel, and the effect of the secondary disturbance was small.