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.