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Based on the basic principle of thermodynamics, an elastoplastic damage constitutive model of concrete is constructed in this paper. The model is realized and verified in FLAC3D, which provides a solid foundation for the study of dynamic response and fatigue damage to the base structure of a heavy haul railway tunnel. The dynamic response and damage distribution of the base structure of a heavy-duty railway tunnel with defects were numerically simulated by the concrete elastic-plastic damage constitutive model. Then, by analyzing the response characteristics of the tunnel basement structure under different surrounding rock softening degrees, different foundation suspension range and different foundation structure damage degree are determined. The results show the following: (1) The elastoplastic damage constitutive model of concrete can well describe the stress–strain relationship of materials, especially with the simulation results of post peak softening being in good agreement with the test results, and the simulation effect of the unloading–reloading process of the cyclic loading and unloading test also meet the requirements. (2) The initial stress field and dynamic response of the tunnel basement structure under the action of train vibration load are very different from the ideal state of the structure design when the surrounding rock of the base is softened, the base is suspended, or the basement structure is damaged. With the surrounding rock softening, basement hanging, or basement structure damage developing to a certain extent, the basement structure will be damaged. (3) The horizontal dynamic stress amplitude increases with the increase in the softening degree of the basement surrounding rock. The horizontal dynamic stress of the measuring point increases with the increase in the width of the hanging out area when the hanging out area is located directly below the loading line. When the degree of damage to the basement structure is aggravated, the horizontal dynamic tensile stress of each measuring point gradually decreases. (4) The maximum principal stress increment increases with the increase in the fracture degree of the basement structure, while the minimum principal stress increment decreases with the increase in the fracture degree of the basement structure, but the variation range of the large and minimum principal stress increments is small. The research results have important theoretical and practical significance for further analysis of the damage mechanism and control technology of the foundation structure of a heavy haul railway tunnel with defects. [ABSTRACT FROM AUTHOR]