The Cryogenian Sturtian and Marinoan glaciations stand as the most extreme climate events in Earth history. Intriguingly, large-scale Mn carbonates characterize the nonglacial interlude of this period in South China. The formation mechanism of Mn carbonates and the potential correlation underlying this temporal association remain elusive. Here, we present an integrated petrographic and geochemical study of drill core materials intercepting the Mn-bearing Datangpo Formation. Rare earth element patterns of these Mn carbonates exhibit positive Ce anomalies and a lack of Y anomalies, which differ from those of modern seawater but resemble marine Mn-Fe oxides. These features, combined with negative carbonate carbon isotope compositions (δ¹³C_carb as light as −9.9 ‰ VPDB), indicate the presence of oxide precursors and the incorporation of light carbon during Mn-carbonate precipitation. Phosphate oxygen isotope ratios (δ¹⁸O_p) of HCl-extractable apatite reveal a ∼4 ‰ difference in the average δ¹⁸O_p between Mn-rich and Mn-poor rocks. We propose that the more positive δ¹⁸O_p of Mn-rich samples may result from the dominance of phosphate released by reductive dissolution of metal oxides or a heavier oxygen isotope signal of surrounding waters with which isotopic equilibrium has been reached. We further illustrate how marine invasions into coastal anoxic basins could have triggered the formation of Mn oxides and highlight the role of glaciation–deglaciation in the development of giant Mn deposits.