Macro hydrophobic clusters and complexes of soybean globular proteins were observed using TEM (Transmission Electron Microscope). Upon unfolding, hydrophobic groups of the proteins became exposed toward the surface of the protein and actively interacted with other hydrophobic groups of other protein molecules, thereby forming hydrophobic bonding. The hydrophobic bonding resulted in hydrophobic protein clusters, the formation of which was affected by the degree of protein unfolding, protein structure, and hydrophobic components. Such hydrophobic clusters followed the global minimum free energy theory and formed spherical like structures with diameters ranging from 100 nm to 3000 nm. Such an understanding lends applicability to many uses in adhesives, molding composites, surfactants for oil-water systems, bio-based interior construction paints and paper coatings, fiber production, and metal powder molding applications.