Hexavalent chromium (Cr(VI)) has attracted much attention due to its high toxicity. In order to improve the efficiency of Cr(VI) removal by adsorption, core-shell structured polyethyleneimine (PEI) functionalized composite nanoparticles (Fe3O4@SiO2-NH2) were synthesized to remove Cr(VI) in water. The chemical structure, morphology and magnetic properties of the nanoparticles were investigated. The effects of initial concentration, contact time, solution pH value and inorganic anions on the Cr(VI) adsorption efficiency were analyzed. The results show that Fe3O4@SiO2-NH2 has an excellent performance in removing Cr(VI), and its maximum adsorption capacity is 251.83 mg/g. The adsorption process is pH value-dependent, spontaneous, and endothermic. Fe3O4@SiO2-NH2 is protonated, and the adsorption of Cr(VI) is completed due to the electrostatic attraction. Also, according to the results by X-ray photoelectron spectroscopy, part of Cr(VI) can be reduced to low-toxic Cr(VI). Fe3O4@SiO2-NH2 has a good reusability after removing Cr(VI) in water, and the duration for effective magnetic separation after the removal is just 50 s.