Groundwater can cause many hazardous problems when a tunnel is excavating. Seepage force acting on the support structure and the tunnel surface cannot be negligible. Under high groundwater table condition, the seepage situation becomes more complex and it is more difficult to control the leakage of groundwater to flow into a tunnel. In the paper, a multiple times grouting method is proposed, and the mechanical deformation behavior of surrounding rock is analyzed using the FLAC3D (Fast Lagrangian Analysis of Continua in 3 Dimensions) software according to the high groundwater table condition of the Hokusatsu tunnel. The results present that multiple times grouting can control leakage and the rock deformation well, compared with one-time grouting condition in rock breaking and high water pressure area. The seepage force decrease around the tunnel and the displacement is controlled effectively. The pore pressure reduces inside the grouting zone using a new kind of grouting material, which is high permeability ultramicro particle cement (average particle size 1.5 μm). In the test fieldwork, the grouting scheme reduces the maximum discharge from 300 t/h to 40 t/h, and there is not obvious deformation and abnormal stress in the tunnel. The multiple times grouting method proposed in this research is verified effectively and can supply a positive experience to on-site construction.