With tetraethoxysilane ［Si(OC2H5)4，TEOS］ and methyltriethoxysilane ［CH3Si(OC2H5)3,MTES］ as precursors, two kinds of methyl-modified silica gels were prepared by the two-step method and co-hydrolysis method. The gels were tested at the small angle x-ray scattering(SAXS) Station of Beijing Synchrotron Radiation Facility(BSRF). We calculated the average particle diameter and the special surface area between the two phases. On the basis of these data the fractal characters of gels were analyzed, and two fractal structures were found in all the samples. The two fractal dimensions indicated two fractal structures on two scales, i.e., from primary SiO2 particles to first-aggregates and from first-aggregates to clusters. Aided by transmission electronic microscope(TEM) we confirmed the two different microstructures of the gels prepared using the two different methods. It can be said that SAXS is a powerful technigue to study microstructures of gel systems by studying its fractal structure.