Silica/polyurethane (SiO2/PU) nanocomposites, prepared by in situ formation of silica from tetraethoxysilane (TEOS) in cationic polyurethane microreactor, are used to modify epoxy resin-based electrophoretic coating. The co-electrophoresis property of silica/PU nanocomposites with epoxy particles is verified by X-ray photoelectronic spectroscopy (XPS) analysis of the electrophoretically prepared membrane. The particle sizes and size distribution in the aqueous paint show a considerable reduction as demonstrated by dynamic light scattering. The surface morphology is investigated by scanning electron microscope. The properties of SiO2/PU-modified electrophoretically prepared membrane have a significant improvement compared to those of unmodified and PU-modified membranes. It is noteworthy that both strength and toughness of the electrophoretically prepared membrane increase considerably due to incorporation of rigid silica encapsulated by tough PU.