Fossiliferous Ediacaran successions of South China, the Doushantuo and Dengying formations and their equivalents, are key to understanding bio- and geological evolution at the Neoproterozoic–Cambrian transition. However, their absolute ages, especially the upper Ediacaran successions, are poorly constrained. SIMS zircon U–Pb dating results in this study suggest that ash beds at the basal and middle parts of the Jiucheng Member (middle Dengying Formation) in eastern Yunnan Province were deposited at 553.6 ± 2.7/(3.8) Ma and 546.3 ± 2.7/(3.8) Ma, respectively. These new dates indicate that the age for the base of Dengying Formation in eastern Yunnan Province is similar to the 550.55 ± 0.75 Ma date, which is from an ash bed at the top of the Miaohe Member and has been regarded as the age for the base of Dengying Formation in Yangtze Gorges area. These dates do not permit a clear test of the two correlation models for the chronostratigraphic position of the Miaohe Member (uppermost Doushantuo Formation vs. middle Dengying Formation), implying that further integrated intra-basinal stratigraphic correlations and more high-resolution chronological data from the upper Ediacaran deposits of South China are required. New dates of the Jiucheng Member constrain the age of the fossil biotas in the middle Dengying Formation and extend the stratigraphic range of Rangea, Hiemalora and Charniodiscus to 546.3 ± 2.7/(3.8) Ma. The geochronology of the Dengying Formation implies that Ediacaran-type fossils preserved in this formation are younger than the White Sea Assemblage and temporally overlapping with the Nama Assemblage.