For improving the larger sidewall roughness of an optical waveguide and exploring the advantages of fractionated oxidation over a single oxidation process, silicon-on-insulator ring and racetrack cavities are prepared using microelectro-mechanical system (MEMS) technology. The silicon-on-insulator ring and racetrack cavities are optimized by single and double oxidation processes, respectively. The relationships among the roughness, scattering loss, and transmission characteristics of an optical resonator are theoretically analyzed and simulated. The experimental results show that, a narrower full-width at half-maximum (FWHM), higher quality factor (Q), and lower transmission loss are achieved by the double oxidation process, compared with those achieved by the single oxidation process, for the same oxidation thickness. This result provides a reference for surface-smoothing research and has a significant influence on the preparation and application of cavities with high Q and low transmission loss in filters, biosensors, optical gyroscopes, and other related fields.