We discovered a novel method to prepare a protein-based hydrogel, that is, a “Three-Dimensional Nanostructured Protein Hydrogel (3D NPH)”, which is composed of protein–polymer hybrid nanoparticles. In this study, we propose a novel protein microarray whose 3D NPH spots were prepared by dispensing a small volume of the solution of protein–polymer mixture on a substrate. The dispensed solution had a short time for cross-linking before its drying-up and the resulting 3D NPH had loosely cross-linked, thin spongy structure. Therefore, the reaction ratio between ligands and analytes was drastically improved in this system compared with the large volume system for Surface Plasmon Resonance (SPR) protein microarray.