The small angle X-ray scattering of organically modified MSU-X silica prepared by co-condensation of tetraethoxysilane (TEOS) and methyltriethoxysilane (MTES) show negative deviation from Debye’s theory due to the existence of the organic interface layer. By exerting correction of the scattering negative deviation, Debye relation may be recovered, and the average wall thickness of the material may be evaluated. The small angle X-ray scattering of organically modified MSU-X silica prepared by co-condensation of tetraethoxysilane (TEOS) and methyltriethoxysilane (MTES) show negative deviation from Debye’s theory due to the existence of the organic interface layer. By exerting correction of the scattering negative deviation, Debye relation may be recovered, and the average wall thickness of the material may be evaluated.