Hydrophobically surface-modified membranes were prepared by adding a fluorine-containing graft copolymer into a microphase-separated membrane consisting of poly(dimethylsiloxane) (PDMS) and poly(methyl methacrylate) (PMMA). This study focuses on the effects of surface characteristics and microphase separation of the surface-modified membranes on their permselectivity for a dilute aqueous solution of benzene in pervaporation. Contact angle measurements and X-ray photoelectron spectroscopy revealed that the addition of a fluorine-containing copolymer produced a hydrophobic surface at the membrane air side due to its surface localization. It became apparent from transmission electron microscopy that adding a fluorine-containing copolymer of less than 1.2 wt % did not affect the morphology of the microphase-separated membrane, but adding the copolymer over 1.2 wt % resulted in a morphological change from a continuous PDMS phase to a discontinuous PDMS phase. The addition of a small amount of fluorine-containing copolymer into the microphase-separated membranes enhanced both the permeability and selectivity for a dilute aqueous solution of benzene in pervaporation because of their hydrophobic surfaces and microphase-separated structures. Specifically, the microphase-separated membrane containing 1.2 wt % of fluorine-containing copolymer concentrated from an aqueous solution of 0.05 wt % benzene to 70 wt % benzene and removed benzene in water very effectively. This paper also discusses the effect of the asymmetric surface structure of the hydrophobically surface-modified membranes on their permselectivity.