In this study, a facile and efficient separation of abundant proteins from bovine blood using core–shell structure nanoparticles with a magnetic core and an immobilized metal affinity ligand iminodiacetic acid (IDA) chelating Ni(II) is presented. Firstly, Fe₃O₄ magnetic nanoparticles (MNPs) were synthesized through a solvothermal method and then were conveniently surface-modified with 3-(methacryloyloxy) propyltrimethoxylsilane as anchor molecules to donate vinyl groups. Next a high density poly(4-vinylbenzylchloride) (PVBC) shell was synthesized on the surface of silica-coated Fe₃O₄ MNPs via distillation–precipitation polymerization. After the PVBC shell reacted with iminodiacetic acid (IDA) in alkaline aqueous solution, the magnetite was charged with Ni²⁺ to form Ni(II)-IDA functionalized hybrid Fe₃O₄@PVBC@IDA-Ni MNPs. Transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA) and a vibrating sample magnetometer (VSM) were employed to evaluate the size, morphology and magnetic property of the resulting magnetic nanospheres. The high saturation magnetization (48.1 emu g⁻¹) provides the materials with the convenience of magnetic separation under an external magnetic field and they can be subsequently reused. The core–shell Fe₃O₄@PVBC@IDA-Ni MNPs exhibit excellent performance in the separation of protein bovine hemoglobin (BHb), and the binding capacity is as high as 1988 mg g⁻¹. In addition, the Fe₃O₄@PVBC@IDA-Ni MNPs can be used in selective removal of abundant protein Hb in the bovine blood samples. This opens a novel route for its future application in removing abundant protein in proteomic analysis.