Millions of tons of hazardous iron oxide residues are produced during the iron purification process of sulphate leaching solutions in nonferrous metals hydrometallurgy industry per year. The generated iron oxide residues, which mainly contain goethite and gypsum precipitates adsorbing the hazardous elements of arsenic, sulfur, zinc, and germanium, pose a great threat to the local ecological environment and human health. A novel method for the treatment and recovery of goethite and gypsum by synthetic magnetic nanoparticles (MNPs) such as alpha-Fe3O4 and gamma-Fe2O3 are proposed to treat the residues efficiently and cost-effectively. MNPs serve as the magnetic crystal nuclei of the goethite precipitates during the iron purification process, and the goethite and gypsum precipitates formed under this condition can be separated in magnetic field. Subsequently, the magnetic crystal nuclei were treated using a rod milling and magnetic collecting to obtain goethite precipitates in order to minimize costs. Both precipitates can be digested as raw materials of iron making and building materials, respectively. Additionally, we found that the separation efficiency of the goethite and gypsum precipitates was much higher when gamma-Fe2O3 was used as the crystal nuclei, indicating that the surface of gamma-Fe2O3 was more favorable for the formation of goethite particles than alpha-Fe3O4.