In order to enhance the dispersion ability of hydrophobic nanoparticles in water while maintaining their unique properties, we utilized poly(ethylene glycol) grafted hyperbranched poly(amido amine) (h-PAMAM-g-PEG) to modify three types of hydrophobic nanoparticle, CdSe, Au, and Fe₃O₄, and transferred them into water to extend their applications in biology. Considering the large amounts of amino groups in hyperbranched poly(amido amine) (h-PAMAM) polymer, complexation interaction between h-PAMAM-g-PEG copolymer and nanoparticles was achieved and ligand exchange between the copolymers and original small molecules ligands occurred. The transferred nanoparticles could be easily dispersed in water with better stability, and their unique properties, such as fluorescence, surface plasmon resonance, and superparamagnetism, were well maintained in the ligand exchange process. In addition, increasing the number of grafted PEG showed a negative effect on the ligand exchange process. Due to the existence of h-PAMAM-g-PEG ligands, the stabilized nanoparticles have improved stability in aqueous and ionic solutions. In the case of CdSe nanoparticles, the h-PAMAM-g-PEG layer leads to a lower cytotoxicity when compared with bare CdSe particles, and they could be directly used in bioimaging.