Polydimethylsiloxane has been dominantly employed as the substrate material for microchip capillary electrophoresis. The poor surface chemistry, however, generates inconsistent electroosmotic flow under the electrophoretic condition, limiting its broader applications. In this work, different polyelectrolytes, including polydiallyldimethylammonium chloride, polyvinyl sulfate, and dextran sulfate, were successfully deposited onto polydimethylsiloxane microchannel surfaces. The polyelectrolyte coated polydimethylsiloxane microchannel showed improved consistency and reproducibility in electroosmotic flow under an electric field over the uncoated native microchannel.