The surface of 500-mm-long microchannels in SiO2 microchips was modified using supercritical CO2 (scCO2) and a biocompatible polymer was coated on it to confer biocompatibility to the SiO2 surface. In this method, the SiO2 surface of a microchannel was coated with poly(ethylene glycol monomethacrylate) (PEGMA) as the biocompatible polymer using allyltriethoxysilane (ATES) as the anchor material in scCO2 as the reactive medium. Results were compared with those using the conventional wet method. The surface of a microchannel could not be modified by the wet method owing to the surface tension and viscosity of the liquid, but it was modified uniformly by the scCO2 method probably owing to the near-zero surface tension, low viscosity, and high diffusivity of scCO2. The effect of the surface modification by the scCO2 method to prevent the adsorption of protein was as high as that of the modification by the wet method. Modified microchips can be used in biochemical and medical analyses.