The high temperature proton exchange (HTPE) method was used to fabricate optical waveguides based on LiNbO$_3$, which gives rise to low propagation loss and high polarization extinction ratio. To characterize the refractive index distribution of the fabricated waveguides, the guided modes of each waveguide were observed using the prism coupling method and then the refractive index profile was calculated by the inverse WKB method with the least square fitting. Finally, we showed how the HTPE parameters such as the temperature of PE, the concentration of lithium additive, and the time of PE effect the refractive index profile.