This study presents simple method for surface modification of hydrophobic poly(dimethylsiloxane) (PDMS) microchannel using combination of silane coupling and photopolymerization. The method spatially modulates the wettability and can fabricate high contrast spatial patterning of microfluidic device wettability. The physical and chemical characteristics are investigated with contact angle, Fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), change of meniscus of water fluid, and spatially selective immobilization of fluorescent dyes. We successfully use our method to selectively modify the surface properties in certain areas of assembled microchannel. Furthermore, our approach allows for the generation of highly monodisperse double emulsions and multiple emulsions containing various numbers of inner droplets.