The ground disturbance caused by the tunnel construction will inevitably have an impact on the upper part of the constructed tunnel structure, and the railroad tunnel requires a very high level of control over the structural settlement deformation. For the problem of double-hole tunnel under the built tunnel, this paper takes Chongqing Mingyue Mountain Tunnel under the built Shanghai-Rong Railway Paihua Cave tunnel and Zheng-Yu Railway tunnel as the engineering background, and starts from the mechanism of ground loss caused by tunnel excavation, firstly, the settlement at the height of the existing tunnel strata is obtained through theoretical analysis, and the new Mingyue Mountain Tunnel under the Shanghai-Rong Railway tunnel is determined to be a more dangerous section. Further simulate and calculate the dynamic excavation process of the new double-hole tunnel underpass, and study the settlement deformation law of the Mingyue Mountain Tunnel underpassing the Hurong Railway Tunnel. According to the requirements of railroad tunnel for settlement deformation control, the new tunnel is determined to be constructed by step method to ensure the safety of railroad tunnel. The shortcomings of the theoretical calculation are analyzed to illustrate the important role of numerical simulation in the evaluation of tunnel underpass projects.