To study the change of the pile foundation displacement during the dynamic excavation of the double-route shield tunnel, three-dimensional simulation of shield tunneling under-crossing pile foundation is performed with a finite element package, PLAXIS 3D. Numerical simulation realizes the step-by-step advancing during shield tunnel excavation by taking into account the influence of earth pressure in soil warehouse, grouting pressure, and friction between the shield and the soil. Apart from that, using consolidation calculation of PLAXIS 3D, the paper evaluate the ground settlement caused by the consolidation of the shield’s own weight on the soil, and further evaluate the impact of the excavation speed on the pile displacement. The calculation results show that the tunnel excavation will cause the settlement, lateral displacement and tilt of the pile foundation, and the overall displacement and tilt of the pile foundation can continue to increase with the progress of the shield tunnel excavation. The sensitivity analysis of construction parameters reveals that: increasing the excavation speed can effectively control the displacement of the pile foundation, but when the excavation speed increases to a certain extent, the impact of the excavation speed on the pile foundation is significantly reduced; The effect of simultaneous excavation of the double-route tunnel on the pile foundation is smaller than that of the separated double-route excavation. These results can serve as a technical reference for similar projects.