The lake ecosystem in the Qaidam Basin is a key carbon “sink” and “source” in the arid region, and its microbial-driven carbon metabolism process has significance for maintaining regional carbon balance and responding to global climate change. In this study，eight typical lakes in the basin were selected. After collecting water and sediment samples，metagenomic sequencing technology and multivariate statistical methods were used to systematically analyze the response of carbon metabolism microbial community structure and carbon sequestration characteristics to changes in environmental factors. The results showed that the alpha diversity index of sediment carbon metabolism microbial community was significantly higher than that in water，except for the Simpson index（P < 0.001）. The carbon metabolism microorganisms in water and sediment were dominated by Pseudomonadota，but Cyanobacteriota was the unique bacteria in water，while Chloroflexota were the unique bacteria in sediment. Total organic carbon（TOC）and normalized water balance index（NWBI）were the most significant driving factors for microbial communities of carbon metabolism in water and sediment，respectively. The carbon metabolism microorganisms in water and sediment were dominated by deterministic processes，but the randomness level of water was significantly higher than that of sediment（P < 0.001）. In addition，the results showed that the gene abundance of microbial carbon fixation pathway in sediments was significantly stronger than that in water（P < 0.05），and the reduced citric acid cycle was the common core pathway of carbon fixation in water and sediments. The functional distribution of microbial communities in water carbon metabolism was mainly regulated by TOC，while sediments were more susceptible to NWBI. This study can provide a reference and supplement for predicting the microbial function evolution of the lake ecosystem in the Qaidam Basin under the background of climate change.