When the deep tunnel passes through a water-rich fault zone, it is prone to disasters such as large deformation of soft rock, which brings great challenges to construction safety. In this paper, a multi-field coupling model is established based on the finite element method (FEM), discrete element method (DEM), and computational fluid dynamics (CFD) method, which can simulate the interaction between structure, fractured rock mass, and flow field. The correctness of the model is verified through on-site monitoring data. On this basis, the stability of the surrounding rock when the Xianglushan tunnel crosses the water-rich fault zone is studied. The results show that: (1) the numerical calculation results based on FEM-DEM-CFD are more accurate and consistent with actual engineering situations compared to FEM-DEM calculation results. (2) The deformation of the surrounding rock is divided into four stages: initial deformation, rapid deformation, slow deformation, and stable deformation. When the excavation distance is less than three times the diameter of the hole, the surrounding rock deformation is severe, and the deformation in this stage reaches 70% of the total deformation. (3) During the excavation process, the "soil arching effect" occurs at the vault position, which gradually enhances with the excavation. (4) The damage of the surrounding rock mainly occurs in the vault position, and the final failure type is mainly shear failure. (5) The numerical model is highly sensitive to mesoscale parameters and lateral stress coefficients. The research results of this paper have certain guiding significance for the safe construction of similar projects.