A PEG-NH2-based environmentally friendly surface modification strategy was developed for PDMS microchips to prevent protein adsorption and to enhance separation performance. PEG-NH2 was synthesized using a modified synthesis procedure. A two-step grafting method was used for PDMS modification. FTIR absorption by attenuated total reflection and contact angle measurements verified the successful grafting of PEG-NH2 onto the PDMS surface. Subsequent EOF Measurements and protein adsorption studies of PEG-modified PDMS microchips revealed noticeable EOF suppression and resistance to nonspecific protein adsorption for more than 30 days. Separation of four FITC-labeled amino acids was further demonstrated with high repeatability and reproducibility. Comparison of electrophoresis of 3-(2-furoyl)quinoline-2-carboxaldehyde-labeled BSA using PDMS microchips before and after surface modification resulted in significantly improved electrophoretic performance of the PEG-modified PDMS microchips, suggesting that our PEG grafting method successfully modified PDMS surface property and prevented adsorption of proteins. We expect that this environmentally friendly surface modification method will be useful for future protein separations with long-term surface stability.