We have discovered a novel method to prepare a protein-based hydrogel, that is, a 'three-dimensional nanostructured protein hydrogel' (3D NPH), which is composed of loosely inter-connected protein-polymer hybrid nanoparticles. The 3d NPH can be easily prepared by spotting a protein/polymer mixture on a substrate. Surprisingly, gold nanoparticles carrying protein molecules easily diffuse into the 3d NPH through pores and spaces. We have shown that the protein chip made by our 3D NPH method has tremendously improved interactions compared with that by direct protein immobilization methods.