A simple and rapid bulk-modification method based on adding an amphiphilic copolymer during the fabrication process was employed to modify PDMS microchips. Poly(lactic acid)-poly (ethylene glycol) (PLA-PEG) was used as the additive substance. Compared to the native PDMS microchips, both the contact angle and the EOF of the bulk-modified PDMS microchips decreased. The effects of the additive loading and the pH on the EOF were investigated in detail. The bulk-modified PDMS microchips exhibited reproducible and stable EOF behavior. The application of the bulk-modified PDMS microchips was also studied and the results indicated that they could be successfully used to separate amino acids and to suppress protein adsorption.