Two kinds of methyl-modified silica xerogels were prepared by mixing SiO2 colloidal suspension deriving from basic-catalyzed hydrolysis of TEOS (tetraethoxysilane) and siloxane polymer solution prepared from acid-catalyzed hydrolysis of MTES (methyltriethoxysilane) or DDS (dimethyldiethoxysilane). The xerogels were tested at the small angle x-ray scattering (SAXS) station of Beijing Synchrotron Radiation Facility. The distribution of pore size, the average size of pores DSAXS, and the thickness of interface layer E were calculated. With the aid of nitrogen adsorption measurement, the pore structure was analyzed. Some micropores were found to be produced in methyl-modified SiO2 xerogels while second-aggregates were constructed through connecting first-aggregates with siloxane polymer of MTES or of DDS. At the same time, methyl groups were attached to the bone of SiO2 clusters and become an interface layer between bone and pore. The interface layer have effects on both pore size and the adsorption of nitrogen in methyl-modified xerogels. Through transmission electron microscope we confirmed that the pore structures of the xerogels were affected strongly by the two different siloxane polymers. SAXS is a powerful technique to study pore structure of xerogel system.