A new environmentally friendly method is developed for preventing nonspecific biomolecules from adsorption on poly(dimethylsiloxane) (PDMS) surface via in situ covalent modification. o-[(N-Succinimdyl)succiny]-o'-methyl-poly(ethylene glycol) (NSS-mPEG) was covalently grafted onto PDMS microchannel surface that was pretreated by air-plasma and silanized with 3-aminopropyl-triethoxysilanes (APTES). The modification processes were carried out in aqueous solution without any organic solvent. The mPEG side chains displayed extended structure and created a nonionic hydrophilic polymer brushes layer on PDMS surface, which can effectively prevent the adsorption of biomolecules. The developed method had improved reproducibility of separation and stability of electroosmotic flow (EOF), enhanced hydrophilicity of surface and peak resolution, and decreased adsorption of biomolecules. EOF in the modified microchannel was strongly suppressed, compared with those in the native and silanized PDMS microchips. Seven amino acids have been efficiently separated and successfully detected on the coated PDMS microchip coupled with end-channel amperometric detection. Relative standard deviations (RSDs) of their migration time for run-to-run, day-to-day and chip-to-chip, were all below 2.3%. Moreover, the covalent-modified PDMS channels displayed long-term stability for 4 weeks. This novel coating strategy showed promising application in biomolecules separation.