Heterogeneous Fenton-like processes using green rusts (GRs) with hydrogen peroxide (H2O2) were studied to decolorize methyl orange (MO) in aqueous solution at an initial pH of 7.0. In this study, two types of crystal structure for GRs, the hydroxycarbonate GR(CO32–) (GR1) and the hydroxysulphate GR(SO42–) (GR2), were synthesized by partial oxidation of Fe(OH)2 suspension under light irradiation and distinguished by X-ray diffraction (XRD) due to different characteristic peaks. In oxidation reactions, decolorization rate of MO, bubbling air through the solution, was about 65% (experiment B), whereas, it was up to 95% in the presence of H2O2 (experiment C) within 60 min. The comparative tests of GR1 and GR2 show that the reduction capability of GR2 is stronger than GR1, which may be due to Fe(II) content and interlayer anions. XRD analysis and Fourier transform infrared spectroscopy revealed that the oxidation end products of GR2 were mainly a poorly crystallized mixture of magnetite (Fe3O4) and hydroxy ferric oxide (FeOOH). However, when GR was immediately oxidized, the weakly crystallized goethite (α–FeOOH) and lepidocrocite (γ–FeOOH) were formed for O2 and H2O2, respectively. Based on the intermediates obtained, a probable decolorization mechanism has been proposed.