Proton exchange waveguides in MgO:LiNbO.3 and LiNbO.3 crystals were fabricated , and the diffusion coefficients for the proton exchange process are obtained. The evolution characteristics of the waveguide index profile in the annealing process are studied. The structural deformation of the proton exchange waveguides in Mg O:LiNbO.3 and LiNbO.3 and the restoration effect of annealing are also studied tho roughly by the x-ray diffraction method and the OH-infrared absorption method. The optical and structural characteristics of annealed proton exchange waveguides in MgO:LiNbO.3 and LiNbO.3 are analysed and compared with eath other.