Z-cut LiNbO 3 crystals were implanted at room temperature with 3.0MeV O ions with a fluence of 6×10 14 ions/cm 2 . The effective refractive index of the guided mode was obtained by the prism coupling technique combined with mechanical stripping (ion beam etching) at room temperature. Surface layers, with thicknesses of 300, 630, 880, 1100, and 1500nm, were removed. The channel spectra of LiNbO 3 waveguides with different etching depths were measured by the RBS technique. The damage profile of the LiNbO 3 waveguide was studied by dechannelling analysis with a multiple scattering function based on the channel spectrum. The refractive index profile was calculated based on the lattice damage ratio. The effective refractive index of the guided mode simulated by BPM showed good agreement with the experiment value.