The Cryogenian Period is featured by episodic global glaciations which likely imposed an extreme and prolonged environmental stress on coeval eukaryotic evolution. However, although the globally widespread diamictite deposits are considered as the major evidence, their glacial nature and related sedimentology still remain debated, preventing our understanding of environmental backdrop for eukaryotic evolution in the Cryogenian. In this study, we conducted a systematic sedimentological investigation on the Cryogenian Nantuo Formation in the Shengnongjia area, South China. The thickness of Nantuo Formation increases from ~2 to ~300 m across the study area, comprising of diamicitite facies, conglomerate facies, lonestone-bearing facies, green siltstone facies and black shale facies. Detailed facies analysis reveals that diamictite unit in western sections were mostly deposited with subaqueous proglacial, and partially deposited with glacially-induced debris flows. Micro-scaled galaxy structures, grain stack, microshear and grain-to-grain contacts were observed in the diamictites of eastern sections, implying that the diamictite might be deposited under subglacial condition. In western sections, abundant dropstones and mud pellets within finely-laminated turbidites occur in the lonestone facies, providing convincing evidence for their ice-rafted origin, although part of them are reworked by turbidity flow. The black shale and green siltstone facie shows the lack of glacially-related features which may represent the glacial retreat system. Given the rapid thickness and facies changes of the Nantuo Formation, we interpret that the Nantuo Formation was likely deposited during deglaciation on a complex palaeotopography by subglacial incised into the bedrock during maximum glacial advances. The diamictite facies to black shale or siltstone facies record a complete deglaciation sequences and the succession in Songluo section contain three cycles of glacier advance and retreat reflecting a dynamic fluctuating ice margin. The Songluo biota in the black shale deposited following glacial retreat represent the survival of macroalgae during the Cryogenian Period. We infer the survival of macroalgae is related to decreasing sediment input and increasing light availability under ice-free condition.