Abstract: Qinghai Lake is the largest saltwater inland lake in China, and its watershed contains a variety of water bodies with different functions. However, differences in microbial community structure and diversity among different water bodies in the Qinghai Lake basin are still lacking in research. This study compares the microbial community structure of Qinghai Lake with that of the lakeside inundation zone. Using 16S rRNA high-throughput sequencing technology, we investigated the similarities and differences in microbial community composition of water bodies under different environmental conditions. The results showed that the highest relative abundance at the taxonomic level in the main lake and the submerged area of Qinghai Lake were Proteobacteria (44.8%), Bacteroidetes (25.9±7.8)%, Cyanobacteria (13.6±5.4)%, Actinobacteria (7.54±9)% and Tenericutes (3.32±2)%. The structure of microbial diversity in the main area of Qinghai Lake did not differ significantly between sites, but differed significantly from the submerged area. The overall microbial diversity was significantly higher in the submerged area than in the main lake. Some of the microbial taxonomic genera showed significant differences in distribution between the two lakes, suggesting adaptations of these bacteria to environmental characteristics. The widespread distribution of Nodosilinea algae in the main lake of Qinghai Lake may play an important role in the carbon cycling process of alkaline lakes in the plateau. The results of the analysis of water chemistry indicators showed that the main chemical indicators affecting the microbiological differences between the two types of water bodies were pH, total phosphorus and water temperature. This study has important implications for gaining insights into how the environment shapes the microbial community structure of brackish water bodies.