Widespread development of microbialites harbors a series of clues about microbial activity, environmental condition, and aquatic chemistry. The Ediacaran-Cambrian transition draws extensive attention on the co-evolution of complex life and Earth's environment but the associated microorganism development has been largely ignored. In this study, we present a high-resolution database with respect to the spatial and temporal distributions of microbialites in China through the terminal Ediacaran to the early Cambrian Period and describe morphological and petrological characteristics of stromatolites and thrombolites in detail to shed light on the evolutionary process of microbial carbonates. Microbialite development experienced two thriving intervals during the Ediacaran-Cambrian transition: latest Ediacaran to early Fortunian, and Cambrian Age 3 to middle Age 4. The columnar and domical stromatolites show no marked morphological changes in the Ediacaran-Cambrian transition, but stratiform stromatolites exhibit a notable decline in Cambrian time, likely caused by increasing bioturbation in the Cambrian shelf environments. Meanwhile, thrombolites evolved to form large and complicated structures in the early Cambrian featured by meter-level mound morphology and columnar-branching microbial forms (fan-like/dendritic structures), likely indicating an improved environmental adaptation (e.g., photosynthesis efficiency and hydrodynamic conditions). Another remarkable change in microbialites is the emergence of large numbers of calcified microbial microfossils preserved within the laminated/clotted mesostructures in Cambrian facies, compared with the Ediacaran forms that lack such unique structural features. For the main control over the Cambrian microbial calcification event, this study stresses again the essential role of seawater chemistry (Mg/Ca molar ratios and Ca²⁺ concentrations) in the formation and preservation of calcified microorganisms based on previous insights and elaborate characteristics of their occurrence and microstructures in China. The transition of the Neoproterozoic “aragonite-dolomite sea” to the Cambrian “calcite sea” (likely widely distributed in Age 3) may have promoted to the generation of an original calcite mineralogy in microbial fossils, which has a stronger ability to resist diagenetic dissolution and substitution (e.g., phosphatization and silicification) than that of the aragonite precursor.