Craft copolymer membranes consisting of both ethanol- and water-permselective components for the separation of aqueous ethanol solutions were prepared by the copolymerization of an oligo-dimethylsiloxane (DMS) macromonomer with methyl methacrylate (MMA). This paper describes the relationship between microphase separation in MMA-g-DMS membranes and their permselectivity for aqueous ethanol solutions by pervaporation. The MMA-g-DMS membranes changed drastically from water to ethanol permselective according to the DMS content. Using a transmission electron microscope, appreciable microphase separation was observed in the MMA-g-DMS membranes. The change in the permselectivity of the MMA-g-DMS membranes could be explained by morphological changes in the microphase separation, based on Maxwell’s model and a combined model consisting of both parallel and series models. Furthermore, image processing of the transmission electron micrographs enabled us to reveal the percolation transition of the DMS phase at a DMS content of about 40 mol %. These results suggest that the continuity of DMS phases in the microphase separation of MMA-g-DMS membranes directly affects their permselectivity for aqueous ethanol solutions.