In this study, protein micropatterns were created on the surface of three-dimensional hydrogel microstructures. Poly(ethylene glycol)(PEG)-based hydrogel microstructures were fabricated on a glass substrate using a poly(dimethylsiloxane) (PDMS) replica as a molding insert and photolithography. The lateral dimension and height of the hydrogel microstructures were easily controlled by the feature size of the photomask and depth of the PDMS replica, respectively. Bovine serum albumin (BSA), a model protein, was covalently immobilized to the surface of the hydrogel microstructure via a 5-azidonitrobenzoyloxy N-hydroxysuccinimide bifunctional linker, which has a phenyl azide group and a protein-binding N-hydroxysuccinimide group on either end. The immobilization of BSA on the PEG hydrogel surface was demonstrated with XPS by confirming the formation of a new nitrogen peak, and the selective immobilization of fluorescent-labeled BSA on the outer region of the three-dimensional hydrogel micropattern was demonstrated by fluorescence. A hydrogel microstructure could immobilize two different enzymes separately, and sequential bienzymatic reaction was demonstrated by reacting glucose and Amplex Red with a hydrogel microstructure where glucose oxidase was immobilized on the surface and peroxidase was encapsulated.