The magnetic separable iron oxide/carbon nanocomposites have been prepared with the two-phase hydrothermal–calcination method. The products were characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The results of XRD and TEM illustrated that the as-prepared nanocomposites were quasi-spherical Fe3O4 or γ-Fe2O3 nanoparticles (∼20 nm) evenly dispersed on the surfaces of carbon membranes. The as-prepared products were used to investigate their promising adsorptive applications in Congo red (CR) removal. According to the Langmuir equation, the maximum adsorption capacities of the Fe3O4/C nanocomposite and the γ-Fe2O3/C nanocomposite for CR were calculated to be 48.1 and 105.3 mg g−1, respectively. This novel synthesis method has the potential to prepare magnetic separable iron oxide/carbon nanocomposites for the removal of CR from aqueous solution.