Mischief Reef has unique landforms and rich biological resources, and its marine microorganisms and fishery resources are being developed and utilized. To understand the bacterial diversity in the aquaculture area of Mischief Lagoon in summer, as well as its correlation with environmental factors, the community structure of seawater bacteria were analyzed through high-throughput sequencing technology, the main environmental impact factors were explored, and its functions were predicted by PICRUSt. The results showed that the bacteria of Mischief Reef lagoon had rich community composition. A total of 29 phyla, 57 classes, 152 orders, 256 families, and 439 genera were detected. The dominant bacteria include Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria. There were differences in the alpha diversity index between the three water layers of each site, but none of them reach a significant level. Using redundancy analysis, it was found that the main environmental impact factors are salinity, COD, COD/NO₃-N, and active silicate. The main functions, determined by PICRUSt functional prediction, included metabolism (amino acid metabolism, carbohydrate metabolism, energy production and conversion), genetic information processing (protein translation and modification, DNA replication, recombination and repair), and information processing (signal transduction mechanism, coenzyme transport, inorganic ion transport). This study analyzes the marine community structure of the Mischief Reef Lagoon aquaculture area in summer and its relationship with factors, providing a scientific basis for understanding the microbial diversity and rational development and utilization of the South China Sea, marine fisheries development and protection, and ecosystem protection.