The Haide tunnel needed to pass through a large number of caves in the construction, and encountered the problems of over limit deformation and collapse caused by heavy rainfall. Based on FLAC3D, an unsaturated seepage module considering rainfall infiltration was developed in this paper. Orthogonal numerical experiments considering three factors of filling medium, karst caves’ location and rainfall intensity were designed. Combined with measured deformation and pressure data, the tunnel’s mechanical characteristics were studied. The conclusions show that the karst caves with different filling medium have an effect on the tunnel deformation, which is mainly caused by the change of pore pressure due to the difference of medium’s gravity, permeability and water holding capacity. The spatial position of the karst cave causes the spatial difference of the mechanical properties of the tunnel. The caves near the arch have a restraining effect on the deformation and stress of the tunnel’s arch, while the caves near the side wall increase the deformation and stress of the lower section of the tunnel. According to the displacement release coefficient, the existence of these caves increases the spatial effect of tunnel construction. Heavy rainfall supplies the groundwater, which then increases the magnitude of the ground stress in a short period of time, finally brings additional bearing capacity to the tunnel structure. When the rainfall enters the well -permeable soil in the cave, the influence of the cave on the tunnel will also be changed.