A novel method for rapid separation and determination of ascorbic acid and uric acid has been developed with a polycation-modified poly(dimethylsiloxane) (PDMS) microchip under a negative-separation electric field. Just by flushing the microchip with aqueous solutions of the polycations, poly(allylamine) hydrochloride, poly(diallyldimethylammonium chloride) or chitosan could be stably coated on the PDMS microchannel surface, which resulted in a reversed electroosmotic flow and thus the rapid and efficient separation of the two substrates. Factors influencing the separation, including polycation category, buffer solution, detection potential and separation voltage, were investigated and optimized. The cheapness, rapid analysis speed and the successful analysis of human urine make this microsystem attractive for application in clinics.