In this study, samples were collected from different types of artificial fish reefs and prevention and control areas in the sea areas of the northern part of Da Changshan Island and the northeastern part of Xiao Changshan Island in the North Yellow Sea. The purpose is to compare the differences in the bacterial communities among different regions, determine the impacts of environmental factors on the bacterial communities, and evaluate the ecological effects of artificial fish reefs on the marine bacterial communities. We obtained a total of 2,128,186 effective sequences and 4321 bacterial operational taxonomic units (OTUs), which were classified into 14 phyla and 76 genera. Proteobacteria were the most abundant phylum across the 32 samples, followed by Bacteroidetes. We found that all samples from the deep-sea control area exhibited the highest bacterial richness. In addition, all samples from the shallow-water concrete reef exhibited high community richness. The distribution of bacterial communities showed differences among different regions. In two specific sea areas, the bacteria in the sediment samples exhibited particularly remarkable characteristics of high diversity. Importantly, environmental factors significantly influence bacterial communities. In seawater samples, salinity (Sal) and dissolved oxygen (DO) were the primary factors affecting bacterial communities. Furthermore, grain size (GS) emerged as the most critical physicochemical factor influencing bacterial communities in sediment. This study compared the characteristics of bacterial communities in different types of artificial reefs and control areas in two marine ranches and revealed the main environmental factors affecting the bacterial communities. This is of great significance for protecting biodiversity and evaluating the ecological effects of artificial reef placement.