The Haide tunnel needed to pass through a large number of caves during con-struction, and suffered from problems such as beyond limitation deformation and even collapse caused by heavy rainfall. Based on FLAC3D, an unsaturated seep-age module considering rainfall infiltration was developed. Orthogonal numerical experiments considering three factors of filling medium, karst caves’ location and rainfall intensity were designed. Combined with measured deformation and pres-sure data, the tunnel’s mechanical characteristics were studied. The conclusions show that the karst caves with different filling medium have an effect on the tun-nel deformation, which is mainly caused by the change of pore pressure because of the difference of medium’s gravity, permeability and water holding capacity. The spatial position of the karst cave causes the mechanical properties of the tun-nel to change a lot. The caves near the arch have a restraining effect on the defor-mation 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 increase the spatial effect of tunnel construction. Heavy rainfall supplies the groundwater, then in-creases the magnitude of the ground stress in a short period of time, finally brings additional load to the tunnel’s structure. When the rainfall enters the well-permeable soil in the cave, it would also change the degree of influence of the cave on the tunnel.