When the tunnel in the certain section of the Nanning Subway Line passes under the lake bottom at a close distance, the left line is excavated by shield method, and the right line is excavated by underground excavation method. In order to study the disturbance effect of the left and right lines of the tunnel on the overlying soil under different excavation methods, the critical overburden thickness above the tunnel is analysed. The FLAC 3D numerical simulation is used to analyse the migration law of the surface soil after the tunnel excavation, and the stress and deformation state of the lining structure and the stability of the surrounding soil after the tunnel is completed. The results show that: The actual overburden thickness of the left and right tunnels met the requirements; after the excavation of the tunnel, the final displacement of the ground surface was within the requirements of the specification, which will not affect the safety of the ground surface and surrounding buildings. The principal stress value of the lining structure was less than the design strength standard value. After the completion of the tunnel, the stress of the lining structure and surrounding soil of the left and right line tunnels did not reach the ultimate strength. The soil deformation and surrounding surface settlement of the left line tunnel met the requirements of the specification, while the soil deformation and upper lake bottom deformation of the right line tunnel increased significantly. The research results are of great significance to the construction of other tunnels under the lake in the future.