Surface modification of inorganic oxide with organic modifiers is an important process in areas of surface and interface engineering. In this paper, we report the hydrophobic modification of SiO2 surface using tetramethyldisilanobiphenyl (DSBP) and tetramethyldisilanobithiophene (DSBT) as new modifiers. Irradiation of an ozone-cleaned glass plate in a toluene solution of DSBP with a low-pressure mercury lamp at room temperature in an argon atmosphere led to the hydrophobic modification of the glass surface. Treatment of a glass plate in the dark at room temperature provided similar hydrophobic surface, although the process proceeded less rapidly. Modification of glass surface was also possible by DSBT, but less effectively. This process with DSBP was applied to the fabrication of the top-contact p-type organic thin film transistor (OTFT) with a pentacene film as the active layer, prepared by vapor-deposition on SiO2/Si surface. Modification of SiO2/Si surface by DSBP led to enhanced mobility, by enlargement of grain size and enhancement of the crystallinity.