Manganese and Fe have similar geochemical properties in the supergene environment. Separation of Mn and Fe is an important process for the formation of high-grade sedimentary manganese deposits. Large-scale manganese carbonate deposits (total reserves of approximately 700 Mt) were formed during the interglacial of the Sturtian and Marinoan in South China. The orebodies are hosted in the black rock series at the basal Datangpo Formation of the Cryogenian period. The Fe contents in ores range from 1.15 to 7.18 wt.%, with an average of 2.80 wt.%, and the average Mn/Fe ratio is 8.9, indicating a complete separation of Mn and Fe during the formation of manganese ores. Here, we present element data of manganese carbonates and sulfur isotopes of pyrite from the Dawu deposit, Guizhou, China, aiming to investigate the separation mechanism of Mn and Fe and the ore genesis. The Fe in ores mainly occurs as carbonate (FeCO3) and pyrite (FeS2). The Mn, Ca, Mg and Fe exist in the form of isomorphic substitutions in manganese carbonate. The contents of FeCO3 in manganese carbonates are similar in different deposits, with averages of 2.6-2.8 wt.%. The whole-rock Fe and S contents have an obvious positive correlation (R = 0.69), indicating that the difference of whole-rock Fe content mainly comes from the pyrite content. The delta S-34(V-CDT) of pyrite varies from 40.0 to 48.3 parts per thousand, indicating that the pyrite formed in a restricted basin where sulfate supply was insufficient and the sulfate concentrations were extremely low. Additionally, the whole-rock Fe content is negatively correlated with the delta S-34 values of the whole-rock and pyrite, with correlation coefficients of -0.78 and -0.83, respectively. Two stages of separations of Mn and Fe might have occurred during the mineralization processes. The reduced seawater became oxidized gradually after the Sturtian glaciation, and Fe2+ was oxidized and precipitated before Mn2+, which resulted in the first-stage separation of Mn and Fe. The residual Mn-rich and Fe-poor seawater flowed into the restricted rift basin. Mn and Fe were then precipitated in sediments as oxyhydroxide as the seawater was oxidized. At the early stage of diagenesis, organic matter was oxidized, and manganese oxyhydroxide was reduced, forming the manganese carbonate. H2S was insufficient in the restricted basin due to the extremely low sulfate concentration. The Fe2+ was re-released due to the lack of H2S, resulting in the second-stage separation of Mn and Fe. Finally, the manganese carbonate deposit with low Fe and very high delta S-34 was formed in the restricted basin after the Sturtian glaciation.