SiO x buffer layer is widely employed in metal-clad Z-cut LiNbO3 optical waveguides to prevent excessive propagation loss and disturbances induced by the direct loading of the metal on the guiding layer. The dependence of propagation loss in proton-exchange LiNbO3 channel waveguides induced by a SiOx buffer layer on the annealing time is studied using a nondestructive measurement method. These studies reveal that the propagation loss is degraded for annealing times of less than 3 h, while it can be improved by about 0.08 dB/cm for annealing times longer than 6 h. By extending the annealing time to 8 h, we demonstrate a propagation loss reduction of 0.09 dB/cm. The physical mechanisms, including surface roughness, refractive index changes, oxidation of the SiOx buffer layer, optical confinement, and surface scattering of the LiNbO3 channel waveguide are also investigated.