Underground large diameter twin water conveyance tunnels which underpass the existing bridges will affect the stability of the bridge foundation and structure. To clarify the impact, a high-precision numerical model of bridge-stratum-pile foundation-shield tunnel is constructed for the fine simulation of bridge pile foundation structure and shield tunneling process. Then the simulation results are combined with an intelligent algorithm-based stratum parameter inversion model to obtain more realistic soil stratum parameters. The results show that the maximum surface settlement caused by shield tunneling is 15.01 mm, and the error of the calculated surface deformation based on inversion is reduced by about 70%, compared with that of the actual monitoring value; the excavation of the twin tunnels will cause secondary settlement deformation on the surface, with the largest secondary settlement found in the area between the two shield tunnels, which accounts for about 60% of the total settlement, and the maximum secondary settlement is 5.06 mm. Moreover, the pile foundations on both sides of the tunnels are greatly affected, with a maximum displacement of 10.03 mm, located at the top of the pile foundation. However, tunnel excavation has a relatively small impact on the stress distribution inside the pile foundation, which is negligible.