Silicon surface imperfection was investigated by an X-ray diffraction technique under the condition of simultaneous specular and Bragg reflections, using the tunability of synchrotron radiation in conjunction with an asymmetric reflection. The surface roughness was the main imperfection on the conventional mechanochemical polished silicon wafer, and this surface imperfection was reduced by a series of sacrificial oxidation procedures. The time-dependent dielectric breakdown (TDDB) characteristics were also improved by these procedures. In this way, the reliability of the metal oxide semiconductor capacitor was dependent on the surface imperfection of the silicon substrate.