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The Ediacaran-Cambrian (E-C) transition period witnessed one of the most important environmental changes in Earth’s history. The western margin of the South China Block (SCB), a shallow-water environment, shows a complete sedimentary record of the E-C transition. Section surveys revealed that dolostone, microbial carbonate, chert, and phosphorite predominantly compose the lithologies of the western margin of the SCB during the E-C transition. Petrological analysis indicates that microbial carbonates in this region exhibit stromatolitic, thrombolytic, cavitated, and sporadic microbial structures. Microbial carbonates with stromatolitic, thrombolytic/cavitated, and sporadic structures correspond to strong, moderate, and weak hydrodynamic conditions, respectively. Microcrystalline dolomites crystallize during the syngenesis stage, while meso- to macrocrystalline and sparry dolomites develop during the burial diagenesis stage. Analysis of major elements and rare earth elements anomalies (δCe: 0.580 ~ 0.753; δEu: 1.234 ~ 1.433) suggests that the siliceous component originates from hot-water sources and is transported into shallow-water environments by upwelling. The absence of a δEu anomaly and the morphology of peloids indicate that the phosphatic component is primarily influenced by biological activity and upwelling. During the Tongwan Movement (545–535 Ma) in the E-C transition period, cyclical upwelling transported increased amounts of deep-source materials into shallow platform waters, leading to higher concentrations of siliceous components and widespread microbial mortality. Following the widespread microbial mortality, the phosphatic component became enriched in deep-water environments. Subsequently, the upwelling transported siliceous- and phosphatic-rich fluids back into the shallow-water environments. The phosphatic component was ultimately assimilated by small shelly fauna and deposited in the phosphatic-rich strata of the early Cambrian period. This study elucidates the origins of complex lithological compositions and the sedimentary evolution model in shallow water environments of the E-C transition period in western SCB, offering evidence for global environmental changes during this period. [ABSTRACT FROM AUTHOR]