【Objective】 Microorganisms play an important role in the biogeochemical cycle of lake ecosystems and are important factors affecting the long-term sequestration of organic carbon in lakes. However, the current understanding of the distribution of sediment microbial communities and their impact on carbon dynamics is still insufficient. 【Method】 In this study, we used high-throughput sequencing to analyze the distribution pattern of microbial communities in sediments of west Dongting Lake. Combined with geochemical parameters such as sediment mechanical composition, total organic carbon, and molecular composition of organic matter, we analyzed the influence of environmental factors on microbial community structure and explored the key factors regulating the structure of sediment microbial communities. 【Result】 Significant differences in microbial community structures were observed among different sediment layers (Bacteria: R² = 0.542, P < 0.001; Fungi: R² = 0.430, P < 0.001). On the one hand, from the shallow layer (0～20 cm) to the deep layer (50～100 cm), the relative abundance of copiotrophic microorganisms (e.g., Proteobacteria) in the sediments significantly decreased while the relative abundance of oligotrophic microorganisms (e.g., Chloroflexi) significantly increased. On the other hand, the abundance of the main functional groups of microorganisms changed significantly with increasing sediment depth. In particular, the functions related to aerobic chemoheterotroph and aerobic ammonia oxidation were significantly more abundant in the shallow sediment than in the subsurface (20～50 cm) and deep layers. The differential distribution of microbial communities in sediments is mainly influenced by changes in organic matter content (Bacteria: R² = 0.532, P < 0.001; Fungi: R² = 0.534, P < 0.001). Our result also revealed that the content of total organic carbon significantly affected the abundance changes of various microbial taxa including Proteobacteria, Chloroflexi, Actinobacteria, Basidiomycota, and Glomeromycota, explaining 76.2% (P < 0.001) and 58.2%(P < 0.01) of the variation in bacterial and fungal community structures, respectively. 【Conclusion】 The variation in the distribution of organic matter was the main reason for the differences in microbial community structure in different sedimentary layers. Thus, this study reveals the role and feedback mechanism of microorganisms in lake ecosystems and is of great significance for exploring the evolution and stability of lake ecosystems.