The waveguide has been fabricated in z-cut ZnO crystal by 2.0 MeV He+ ion implantation at doses of 2×1016 ion/cm2 at room temperature. The dark modes of the waveguide were measured by the prism-coupling method with the wavelength 633 nm before and after annealing in air. It is found that there is no dark mode after annealing in air，which means that the lattice damage is considerably reduced, and a completely recovery of lattice structure can be expected by further annealing treatment. TRIM ′2003 code was used to simulate the damage profile in ZnO crystal by 2.0 MeV He+ ion implantation, and profile of lattice damage versus depth was obtained. The refractive index profiles of the waveguide were reconstructed using reflectivity calculation method，It is found that a positive change of refractive index happens in the guiding region, and an optical “barrier” of low refractive index is formed at the end of the ion track，and also found that the shape of the refractive-index profile are quite similar to that of the damage distribution, which provides a vivid proof that the lattice damage produced by nuclear collisions should be most responsible for fabricating of waveguide.