We report the modification of amine-functioned Fe3O4 nanoparticles (provided by the Laboratory of Bio-Medical Materials of University of Science and Technology Beijing) with polyethylenimine (PEI) using glutaraldehyde (GA) as a linker to increase the concentration of primary amine groups on the surface. The resultant Fe3O4–PEI NPs with immobilized iminodiacetic acid (IDA)–Cu2+ groups were applied to investigate the adsorption capacity and selectivity of model proteins: bovine hemoglobin (BHb) and bovine serum albumin (BSA). The Fe3O4–PEI NPs were characterized by transmission electron microscopy (TEM), vibrating sample magnetometer (VSM), particle analyzer, attenuated total reflection-Fourier transform infrared spectroscopy (ATR–FTIR), ninhydrin colorimetry and thermogravimetric analysis (TGA). The results showed that the well dispersed Fe3O4–PEI NPs had an average size of 172.6nm and were super-paramagnetic with saturation magnetization of 71.11emu/g. The characteristic peaks of PEI appeared in the ATR–FTIR spectra of Fe3O4–PEI NPs. The study of zeta potential measurement presented that the isoelectric points of the Fe3O4–PEI NPs increased to 10.5. Ninhydrin colorimetry analysis of primary amine groups showed that the concentration of primary amine groups on the surface of Fe3O4–PEI NPs increased to 0.45mmol/g and that of TGA is 0.53mmol/g. These results showed that PEI had been successfully modified on the surface of amine-functioned Fe3O4 NPs and the concentration of primary amine groups was significantly increased. The analysis of protein adsorption indicated that the adsorption capacity of BHb was up to about 6000mg/g and that of BSA was only about 2000mg/g, which was about one third of that of BHb. The research on the selectivity of protein adsorption was conducted by HPLC. The result showed that the adsorption capacity of BHb was 2.5 times as high as that of BSA, which further proved Fe3O4–PEI–Cu2+ NPs shows specific adsorption for proteins. These properties suggested the potential of the Fe3O4–PEI–Cu2+ NPs as protein adsorbent.