Developing high-performance materials for efficient isolation of proteins is of great importance. Herein, the authors synthesized a series of magnetic Fe3O4@PS-ANTA-M2+ (M = Ni, Co, Cu and Zn) nanospheres, consisting of fine Fe3O4 nanoparticles encapsulated by functionalized polystyrene shell, where metal ions were complexed by Nα, Nα-Bis(carboxymethyl)-L-lysine hydrate for selectively immobilizing histidine (His)-tagged proteins. The structures of the Fe3O4@PS-ANTA-M2+ were studied by field scanning electron microscopy, transmission microscopy, Fourier transform infrared spectroscopy, thermogravimetric analysis, X-ray photoelectron spectroscopy and vibrating sample magnetometer. The adsorption performance of the Fe3O4@PS-ANTA-M2+ was studied using bovine hemoglobin as a model protein. The thermodynamics of the binding process was studied by isothermal titration calorimetry tests. The resulting Fe3O4@PS-ANTA-Cu2+, Fe3O4@PS-ANTA-Ni2+, Fe3O4@PS-ANTA-Co2+ and Fe3O4@PS-ANTA-Zn2+ possessed adsorption capacities of 21200, 8080, 6640 and 5360 mg g−1, respectively, rendering them as the best adsorbents for protein purification. The adsorption isotherm was better fitted by Langmuir equation. To verify the selectivity, the Fe3O4@PS-ANTA-M2+ was practically employed to isolate His-tagged proteins from cell lysate. The results indicated that the samples showed outstanding adsorption capacity, selectivity and stability, and facile regeneration and separation, outperforming a commercial NTA-Ni column. These findings suggested that the Fe3O4@PS-ANTA-M2+ showed promising applications for specifically isolating proteins from complex biological systems.