With the rapid development of tunnel construction in China, there are constantly emergence of high-difficulty tunnel projects with overlapping or staggered arrangements. Based on the overlapping tunnel project of the upper and lower layers of Bajiaogou on the Chongqing East Ring Railway, through the method of numerical simulation, a number of working conditions have been established for different typical cross-sections, and the changing laws of tunnel vault displacement, invert deformation and horizontal convergence of transverse braces during the construction of overlapping tunnels, and stress distribution characteristics of secondary lining under corresponding non-synchronous excavation conditions are studied. And combined with the law of formation stress change caused by construction and the distribution of plastic zone, the stratum disturbance effect of the excavation process is analyzed. The results show that: (1) The construction of the upper tunnel at different sections mainly caused the settlement of the vault and the convergence of the clearance of the lower tunnel, but the impact on the invert part was small. The construction should focus on the settlement of the vault and the convergence of the clearance; (2) When the upper and lower tunnels are close to each other, the construction of the upper tunnel will cause the lower tunnel to bulge to a certain extent, but with the increase of the distance between the two tunnels, the rebound degree will gradually decrease until settlement. Based on this, the corresponding construction stratum disturbance control measures are proposed, so as to optimize structural design and guide on-site construction services, and provide reference and reference for similar projects in the future.