Core-shell magnetic Fe3O4@C nanospheres functionalized with active chemical groups were synthesized via a one-step template-free solvothermal process and employed to remove hexavalent chromium (Cr(VI)) in aqueous media. The structure of Fe3O4@C nanoparticles could be effectively adjusted by the concentration of precursor. The Fe3O4 core possessed a high magnetism for the convenient separation of Fe3O4@C from aqueous solution, and high porosity and abundant functional groups (-OH, -COOH, and C=C) of carbon layer contributed to a superior performance on Cr(VI) removal. Therein, Cr(VI) ions could be efficiently adsorbed into the carbon layer and reduced to trivalent chromium (Cr(III)) mainly by C=C, and the resulting Cr(III) were chelated by the -COOH group. Noteworthy, the carbon layer thickness, pore size, and amount of chemical groups significantly increased with the increase of Fe3O4@C particle size resulting in a rising removal efficiency on Cr(VI). This study provides a promising approach for removing Cr(VI) and may have a huge application potential.