Abstract The Cryogenian (ca. 717–635 Ma) snowball Earth glaciations ended with the precipitation of “cap” carbonate successions with negative carbon isotope (δ13Ccarb) values, which have been explained by the addition of various 13C-depleted carbon sources in the deglacial process. These arguments assumed that marine dissolved inorganic carbon (DIC) was enriched in 13C in the synglacial ocean. However, this assumption has not yet been tested, because the synglacial ocean chemistry is unknown. In this study, we carried out detailed analyses of the petrology, carbonate carbon (δ13Ccarb) and oxygen (δ18Ocarb) isotopes, organic carbon (δ13Corg) isotopes, major and minor elemental compositions (Ca, Mg, Mn, Fe, Sr), and iron speciation (total Fe, highly reactive Fe, pyrite Fe) of the carbonate layers (also called synglacial carbonate layers) from the Nantuo Formation (ca. 650–635 Ma) on the Yangtze block, South China. Petrographic observations indicated that the synglacial carbonate comprises dolomicrite, mud-crystal powder dolomite, lime dolomite, and dolomitic limestone, supporting an authigenic carbonate origin, and thus, it potentially recorded the ocean chemistry during the Marinoan ice age. The synglacial carbonate is characterized by extreme Mn enrichment, low Fe/Mn ratios, and low δ13Ccarb (−7‰) values. High Mn contents and low Fe/Mn ratios imply marine redox conditions favoring Mn2+ accumulation and Fe2+ oxidation, while low δ13Ccarb values might be attributed to CO2 degassing of submarine volcanoes as well as low primary burial during the glaciation. Since the δ13CDIC value of the synglacial ocean was lower than the δ13Ccarb values of most cap carbonates, we infer the addition of 13C-enriched DIC or removal of 12C during cap carbonate precipitation, such as through carbonate weathering or organic carbon burial. These findings provide new insights into the nature of Cryogenian glaciation, the origin of cap carbonates, and the aftermath of global glaciation.