A comprehensive study on the accretion and diagenesis of the Permian-Triassic boundary microbialites is conducive to a better understanding of the ecological community after the end-Permian mass extinction. Here we studied the special microbialite sequences at the Tianba section of Leye isolated carbonate platform, South China Block. The microbialites are shown as small columnar stromatolites, stromatolitic thrombolites, spotted thrombolites, and domical digitate thrombolites in an ascending order. Thin section analyses, coupled with cathodoluminescence photos and oxygen isotopic data, reveal that all types of microbially-mediated laminae/clots are partly recrystallized. Layers of the Polybessurus-like fossils commonly occur in the recrystallized fabrics of stromatolitic laminae. However, the Polybessurus-like fossils are rare in quantity and generally fragmentary and structureless in stromatolitic clots and spotted clots. Such taphonomic features are likely interpreted as the early decomposition by heterotrophic bacteria in an oxygen-depleted microenvironment caused by rapid accumulations of organic matter in the calm water. More enrichments of C-13 in the laminae of stromatolite and in the clots of stromatolitic thrombolite and spotted thrombolite than in adjacent interstitial matrixes signify the photosynthesis-dominated isotopic fractionation during the growth of microbial communities. Rare calcimicrobial structures but many calcite crystal fans were found in the C-13-depleted digitate clots. These phenomena indicate that seawater on the carbonate platform was C-12-enriched and supersaturated, accelerating carbonate precipitations and decompositions of organic matter within the microbial community. Different preservations of the Polybessurus-like fossil revealed the complicated microbially-dominated sedimentation and post-depositional diagenesis in the abnormal seawater after the catastrophe.