Surface modification offers an efficient and economical route to installing functional groups on a polymer surface. This work demonstrates that primary amine groups can be introduced onto a polymer surface via Buchwald-Hartwig amination, and the functionalized substrates can be chemically bonded to produce functional microfluidic devices. By activating the C-Cl bond in commercially used poly(chloro-p-xylylene) (parylene C) by Pd catalyst and substituting Cl with the amine source, the amine groups are successfully installed in a facile and recyclable manner. The substrates can be covalently bonded with each other via amine-isocyanate chemistry, providing much higher bonding strength compared to previous methods based on noncovalent adhesive coatings. As a result, transparent and flexible microfluidic channels can be fabricated that are compatible with organic solvents and high pressure. Retention of amine group reactivity in the channel suggests the potential of this methodology for the surface immobilization of functional molecules for microfluidic reactors and biosensors.