Ediacaran cap dolostone atop Marinoan glacial deposits contains complex sedimentary structures with extremely negative δ13Ccarb values in close association with oscillations in palaeoclimatic and oceanographic proxy records. However, the precise geological, geochronological and geochemical context of the cap dolostone is not clarified, which hampers us from correctly interpreting the extremely negative δ13Ccarb values and their causal relationships with the Snowball Earth hypothesis. In this study, we conducted detailed in situ geochronological and geochemical analyses on the calcite within the cap dolostone from the Ediacaran Doushantuo Formation in South China in order to define its formation and relationship to the Snowball Earth hypothesis. Petrographic observations show that formation of dolomite pre-dates precipitation of calcite and pyrite, which pre-dates quartz cementation in the basal cap carbonate. Calcite cement within the cap dolostone yielded a U–Pb age of 636.5 ± 7.4/17.8 Ma (2σ, MSWD = 1.6, n = 36/40), which is within uncertainty of a published dolomite U–Pb age of 632 ± 17 Ma (recalculated as 629.3 ± 16.7/22.9 Ma). These age constraints negate the possibility that the calcite cement was formed by late Ediacaran or Cambrian hydrothermal activity. The rare earth element distribution patterns suggest a dominant seawater origin overprinted by subsequent early Ediacaran hydrothermal activity. The combined age, petrographic and geochemical data suggest oxidization of methane clathrates in response to complicated interplay between eustasy and isostatic rebound and hydrothermal fluids.