With the rapid progress of urbanization in China, the commercial areas along the subway are developing rapidly, and this trend makes more and more pit projects face the problem of crossing the subway tunnel. This paper relies on an engineering case of the impact of pit excavation on the tunnel above a subway operation section, and uses on-site monitoring and numerical simulation methods to carry out an in-depth study on the deformation of the subway tunnel directly underneath the operation of pit excavation. After verifying the reliability of the numerical model, three-dimensional finite element software is used to simulate and analyze the pile diameter, pile spacing, number of piles in rows, and a variety of new methods of composite preventive and control measures, to further optimize the pit excavation and support scheme to ensure the safety and stability of the subway tunnel. The optimum pile length, pile diameter, pile spacing and number of piles are determined for the project to control the uplift of the tunnel during foundation pit excavation. At the same time, the control effect of two new methods, namely, expanded bottom piles and guided drilled pipe, is simulated and analyzed in similar projects, which provides a reliable construction theoretical basis and construction scheme reference for similar pit excavation above existing tunnels.