Abstract Multicellular animals first appeared on the earth during the Ediacaran period. However, the relationship between the abrupt biological evolution and environmental changes is still ambiguous. In order to examine seawater temperature and the carbon cycle through the Ediacaran, we analyzed the carbon and oxygen isotope compositions of carbonate rocks from drill cores from the Three Gorges area, South China. Importantly, the core samples include the Nantuo tillite, corresponding to the Marinoan glaciation, through the Doushantuo to the lower Dengying Fms. in ascending order. The δ13C profile displays five positive and five negative anomalies (PI-1 to 5 and NI-1 to 5), and the oxygen isotopes display very high absolute values around 0‰ with the highest at + 1.83‰. The combined δ18O and δ13C chemostratigraphies display both positive and negative correlations between the δ18O and δ13C values. The occurrence of the negative correlations supports the preservation of primary δ18O and δ13C values. The sample NI-4 has a negative correlation of the δ18O and δ13C excursions. The correlation supports a primary signature for both δ18O and δ13C variations. The positive δ18O excursion, accompanied by evidence of a eustatic sea-level fall, provides direct evidence for global cooling in the mid-Ediacaran; the 580 Ma Gaskiers Glaciation is a potential candidate for this global cooling event. The negative δ13C excursion was possibly caused by an increase in remineralization of dissolved organic carbon (DOC) due to enhanced continental weathering during the glaciation. Sample NI-5 is characterized by very low δ13C values, down to − 10‰, corresponding to the Shuram-Wonoka-Pertatataka Excursion. The cause of the δ13C negative excursion is still not clear. However, a ubiquitous occurrence in excursions worldwide, and the lower δ13C values in deeper sections favor the enhancement of remineralization and respiration rather than secondary alteration, a restricted sea environment and lithification in coastal areas.