A metal complex-protein composite comprising apohemoglobin, apoheme oxygenase, apocatalase or apoferrin having cavity and a metal complex has a specific structure that the metal complex is received in the cavity of the apoprotein. The metal complex is prepared by complexation of a metal ion, which is selected from the group consisting of rhodium, ruthenium, and palladium, with a ligand. The metal complex-protein composite functions as a hydrogenation catalyst of an olefin in water. The metal complex-protein composite is thus effectively applied to hydrogenation of water-soluble subtrates and has enviromental advantages over organic solvents.