This paper demonstrates a simple, one step, and low cost surface modification technique for producing cyclic olefin copolymer (COC) polymer-based microcapillary electrophoresis chips consisting highly hemocompatible microchannels by UV-photografting with N-vinylpyrrolidone (NVP) monomer. An optimal condition has been identified to achieve the best surface grafting process. It has been found that this surface treatment enables extremely high surface wettability, hemocompatibility, and bond strength to the microchannels. The surface grafting was confirmed by attenuated total reflection Fourier transform-infrared spectroscopic (ATR-FTIR) study. In vitro protein adsorption using fluorescent labeled bovine serum albumin (FITC-BSA) into the COC microchannel results indicates that the modified chips have excellent protein resistance ability because of the increase of surface hydrophilicity. Hence, the modified chips showed fast, reproducible and high efficient separations of proteins (up to 51,000 theoretical plates per meter). Moreover, this surface modification process show no loss in the optical transparency to the modified microchannel surfaces: an important requirement for real capillary electrophoresis since the fluorescent intensity is directly related to the amount of adsorbed protein on the surface. Therefore, we believe that this simple and promising route of surface modification could be very useful for developing high performance COC microfluidic devices for the separation of proteins, amino acids, and other biomolecules.