We report the facile hydrothermal synthesis and surface functionalization of branched polyethyleneimine (PEI)-coated iron oxide nanoparticles (Fe3O4-PEI NPs) for biomedical applications. In this study, Fe3O4-PEI NPs were synthesized via a one-pot hydrothermal method in the presence of PEI. The formed Fe3O4-PEI NPs with primary amine groups on the surface were able to be further functionalized with polyethylene glycol (PEG), acetic anhydride, and succinic anhydride, respectively. The formed pristine and functionalized Fe3O4-PEI NPs were characterized via different techniques. We showed that the sizes of the Fe3O4-PEI NPs were able to be controlled by varying the mass ratio of Fe(II) salt and PEI. In addition, the formed Fe3O4-PEI NPs with different surface functionalities had good water dispersibility, colloidal stability, and relatively high R2 relaxivity (130-160 1/(mM·s)). Cell viability assay data revealed that the surface PEGylation and acylation of Fe3O4-PEI NPs rendered them with good biocompatibility in the given concentration range, while the pristine aminated Fe3O4-PEI NPs started to display slight toxicity at the concentration of 50 μg/mL. Importantly, macrophage cellular uptake results demonstrated that both PEGylation and acetylation of Fe3O4-PEI NPs were able to significantly reduce the nonspecific macrophage uptake, likely rendering the particles with prolonged circulation time. With the proven hemocompatibility and rich amine conjugation chemistry, the Fe3O4-PEI NPs with different surface functionalities may be applied for various biomedical applications, especially for magnetic resonance imaging and therapy.