The Cu(I)-catalyzed alkyne-azide [2 + 3] cycloaddition has been demonstrated to be an effective and orthogonal conjugation reaction to covalently immobilize biomolecules on magnetic nanoparticles (MNPs). The azido group on the MNP surface provides better conjugation efficiency with alkynated molecules. Moreover, the C-terminal alkynated protein was site-specifically immobilized on MNP. The protein binding activity presented by site-specific immobilization is higher than that by random amide bond formation.