In order to explore the diversity of bacterial community structure and its influencing factors in the shallow sea area of the Haizhou Bay, both surface and bottom water samples from six sites in the bay were selected and analyzed based on high-throughput sequencing technology. The results showed that the abun-dance and diversity of bacterial communities in the bottom water samples were better than those in the sur-face water samples. There was difference in the evolutionary direction of bacterial communities between the bottom and surface water samples, but the difference was not significant between the two bacterial communi-ties. A total of 2 491 operational taxonomic units (OTUs) were detected in the Haizhou Bay, belonging to 32 phyla, 74 classes, 116 orders, 200 families and 364 genera. At the phylum level, the dominant bacteria in the bay were Proteobacteria, Bacteroidetes and Cyanobacteria. Ammonium (NH4-N) and chlorophyll (Chl) were found to be the main environmental factors affecting bacterial community structure. The study demonstrated that the diversity and distribution of bacterial community structure in the shallow sea area of the Haizhou Bay had a certain correlation with environmental factors, which provided a theoretical basis for the sustaina-ble development of the shallow sea ecosystem in this area.