Monodisperse nanostructured Fe3O4/ZnO microrods were successfully prepared by an economic one-step synthesis route. The formation of nanostructured Fe3O4/ZnO microrods was evident from the detailed structural and elemental analysis by field emission scanning electronic microscopy, transmission electron microscopy, Raman spectra and X-ray photoelectron spectroscopy measurements. The formation mechanism of the hexagonal Fe3O4/ZnO microrods was carefully discussed. The removal of toxic metal ions experiments display that Fe3O4/ZnO heterostructures show the best removal efficiency compared with pure ZnO and Fe3O4 structures, and the photocatalytic experiments show that the Fe3O4/ZnO heterostructures display the excellent photocatalytic activity decomposing Rhodamine B (100% after 40 min).