The mechanisms of flue-gas desulfurization using high and low-grade natural manganese oxide ores were comparatively studied. Both manganese oxide ores exhibit good desulfurization capabilities with SO2 content in the effluents less than 30 ppm, but the low-grade ores show the much better desulfurization capability. XRD and SEM/EDS results reveal that the MnO2 absorbs the SO2 to convert to MnSO4. The SO2 give prior to react with the surface MnO2 and the produced MnSO2 enriched on the surface leads to the gradually decrease of the SO2 removal rate during desulfurization process. The better desulfurization capability of the low-grade ores is ascribed to the more dispersive MnO2 due to the poriferous/lax internal tunnel structure, and the embedded inert SiO2 shows better support effects to avoid pore structure blocking, which is favorable for enhancing the diffusion of the SO2 and desulfurization reaction process. This study is of significance in the comprehensive utilization of the low-grade natural manganese oxide ores, environmental protection and even the preparation of the desulfurization catalyst with MnO2.