The Lower Yangtze region in South China plate was located near the equator during the Early Permian, where the shallow-water carbonates of the Qixia Fornation widely developed. The latter were subsequently replaced by the black shale and siliceous rocks of the Gufeng Formation, representing a carbonate platform drowning event at the end of Early Permian. In this study, the carbonate microfacies and carbon isotopic stratigraphy of the Qixia and Gufeng formations were systematically studied in the Pingdingshan section of Chaohu, Anhui Province and Zhengpanshan section of Jurong, Jiangsu Province in order to explore the mechanism of this depositional event. Microfacies data shows that the uppermost of the Qixia Formation can be divided into 9 microfacies, belonging to the inner ramp to middle ramp environment. The lowermost of the Gufeng Formation can be divided into 5 lithofacies, indicating a deep-water basin environment. The depositional environment and paleo-water depth at the boundary between the Qixia and Gufeng formations changed obviously, representing the drowning event of the carbonate platform during the Latest Early Permian. At the same place, sudden drop in the content of calcium carbonate, negative carbon isotope excursion and obviously positive carbon isotope of organic excursion indicate the suddenness and eventuality of carbonate platform drowning. The results show that there is a mirror image relationship between δ13Ccarb of carbon isotope and δ13Corg of organic matter. Carbon isotopes of carbonate and organic matter show decoupling changes of negative and positive excursions, respectively, which may be the result of terrigenous organic matter input. We suggest that the drowning of carbonate platform may be caused by relative sea level rise.