Manganese sulfate, as preparation of manganese dioxide industrial raw material, is obtained upon desulfurization with manganese ore. However, a byproduct, manganese dithionate (MnS2O6) will debase the purity and spoils the recovery of the product. In order to find out the conversion mechanism of MnS2O6 during the ozonation process, we investigated the factors affecting the decomposition rate of MnS2O6, including ozone content, manganese dithionate concentration, sulfuric acid concentration, and reaction temperature. The results confirmed that the conversion rate of MnS2O6 is increased with the increasing of the four factors. There were two sections of MnS2O6 ozonation: (1) Mn2+ was directly oxidized to MnO2; (2) SO42− was obtained by the catalytic oxidation of S2O62− with O3. Meanwhile, the total activation energy of the ozonation kinetics equation of the ozonation reaction was 177.28 kJ mol− 1 according to kinetics analysis. The oxidation experimental results indicated that the oxidizer (O3) was not only beneficial to enhance the disproportionation of MnS2O6, but also provided a way to prevent the secondary pollution, SO2 gas releasing.