The removal of high concentration flue gas sulfur dioxide (SO2) using manganese carbonate ore desulfurization (MCO-FGD) is a promising route that combines economic benefits and pollution control. However, the problems of intermediate oxidation and by-product control have plagued the industrial application of the MCO-FGD technique for a long time. Based on the fact that there is symbiosis of manganese and iron in natural manganese ore, in this study, small amounts of Fe(III) and MnO2 were introduced into the MCO-FGD reaction system to enhance the oxidation of SO2 to SO4− and suppress the manganous dithionate (MnS2O6) by-product generation. The results suggested that the addition of Fe(III) led to the generation of potent oxidant Mn(III) in the reaction system, which accelerated the generation of SO3−• radicals and, thus, enhanced the oxidation of SO2. Under the optimum reaction conditions, the 2.0% of inlet SO2 could be removed to 62 ppm, obtaining 90.1% manganese leaching efficiency, and the concentration of MnS2O6 in the desulfurized liquid was kept below 2.5 g/L after a six-stage desulfurization. The results are of great importance for the sustainable development of the manganese metallurgical industry, which provides theoretical and technical support for the recycling of sulfur and manganese. The influences of different operational conditions on SO2 removal, the catalytic mechanism, and manganese leaching were studied to provide theoretical and technical support for resourceful MCO-FGD technology.