Proton-exchange process causes the increase of extraordinary refractive index in 5 mol% MgO:LiNbO3 crystal, and the existence of MgO does not affect the step-like index profile of LiNbO3 proton-exchanged waveguide. Large propagation lose and instabilities of effective index are present in MgO-doped waveguides fabricated by conventional proton-exchange process, but these drawbacks can be aparently improved by post-annealing treatment.