To investigate the deformation and stability of the rock surrounding a tunnel excavated through layered rock, a three-dimensional numerical simulation was conducted to compare and analyze the right line of the YD2K100+560–630 two-stage docking cross-section of the Yuelongmen Tunnel using a ubiquitous joint model. Based on 3-D numerical simulations, the following conclusions were drawn: (1) The excavation on the construction entrance side significantly disturbed the construction exit side, and the exit side was more disturbed in the steeply dipping layer than in the gently dipping layer. (2) The influence of the dip angle of the laminae on the uplift of the tunnel invert was greater than the influence on the tunnel vault settlement when the laminae were oriented perpendicular to the trend of the tunnel and two-stage docking excavation was used. (3) When two-stage excavation was applied to gently inclined laminated rock, there was an obvious disturbance to both the top of the tunnel (less than one time the diameter of the through face; and to the bottom of the tunnel within 0.5 time the diameter of the through face on the side with the stopping construction exit side during the tunnelling process. When tunnel excavation was conducted against the trend of the layer, there was obvious disturbance to the top of the tunnel within 0.5 time the diameter of the through face and to the bottom of the tunnel within one time the diameter of the entrance face) on the construction exit side during the tunnelling process due to the presence of laminae. The excavation on the construction entrance side significantly disturbed the construction exit side. When docking and penetrating layered rock tunnels, priority should be given to docking and penetrating in the direction corresponding to the layers, and temporary support on the exit side should be strengthened to ensure the deformation stability of the surrounding rock mass.

Due to the long-term coupling effect of a train load and groundwater, the surrounding rock at the tunnel bottom will soften in a certain range and the mechanical parameters of the surrounding rock will decrease, causing the uneven distribution of the confining pressure at the tunnel bottom and affecting the base concrete structure service life. In this research, the method of combining field tests and numerical simulation is adopted, and the vertical displacement, vertical acceleration, and maximum and minimum principal stresses are used as evaluation indicators. The dynamic response law of the base structure with the softened surrounding rock of the heavy-duty train is analyzed, and the Miner linear cumulative damage theory is introduced to obtain the service life of the tunnel bottom structure under different softening conditions. The results show that with the decrease in the softening coefficient and the increase in the softening thickness of the bedrock, the displacement, acceleration, and principal stress response indexes of the structure increase by varying degrees, and the service life of the base structure decreases almost linearly. The maximum vertical displacement, acceleration, and tensile stress are located directly below the track, and the maximum compressive stress is located at the connection between the inverted arch and the side wall. According to the predicted value of the service life, the reliability of the base structure is divided into four levels: safety, warning, danger, and serious danger.