Widespread fibrous dolomite cements in upper Ediacaran Dengying Formation’s botryoidal dolomite were traditionally thought to form through secondary processes, but recent studies indicate they were likely the direct products of unique “dolomite seas” conditions. To elucidate botryoidal dolomite’s formation and the unique “dolomite seas,” it’s vital to date the age variability in its dolomite cements via absolute methods. In this study, we performed the first comprehensive geochronological and geochemical (C-O-Sr-REE) analyses on a representative botryoidal dolomite hand specimen PTHB-1, which is divisible into three distinct components: microbialite matrix, fibrous marine dolomite, and crystalline dolomite. Through in-situ laser-ablation ICP-MS U-Pb analyses of 720 meticulously selected laser spots across the specimen, we obtained a dataset of 14 U-Pb age determinations for the various dolomite cements. Notably, ten laminae of U-enriched fibrous dolomite cements yielded ten high-precision U-Pb ages bracketing a time range between 550.1 ± 8.0 Ma and 542 ± 14 Ma (weighted mean 546.8 ± 3.2 Ma), aligning chronologically with the stratigraphic age interval (551.1–542 Ma). These findings, coupled geochemical signatures and petrographic evidence, suggest that the fibrous dolomite cements were initially direct marine precipitates, challenging previous secondary genetic interpretations. This revelation points to a short-lived “dolomite sea” existed in the terminal Ediacaran Ocean in the upper Yangtze region. Conversely, the later stages of vug-filling crystalline dolomite cements exhibit pronounced positive Eu and Y anomalies along with lower δ¹³C and δ¹⁸O, indicating hydrothermal fluid precipitation. Our results reveal at least three phases of crystalline dolomite cements at ca. 411 ± 17 Ma, 358.7 ± 6.1 Ma, and 257.2 ± 8.4 Ma, respectively, contributing significantly to the modification of reservoir properties. The insights gleaned from this research provide crucial chronological data for comprehending the formation and evolutionary history of botryoidal dolomite reservoirs, with substantial implications for hydrocarbon exploration efforts.