The high-throughput sequencing technology was used to analyze the community composition of ballast water samples collected from three vessels which conducted the seawater exchange in international sea and from one vessel in which the ballast water was exchanged at offshore. A total of 27 phyla, 61 classes, 138 orders, 249 families,481 genera and 836 species were detected. The ballast water samples collected from the far shore of the Yellow Sea possessed the largest number of bacterial species detected, up to 564 species; the number of ballast water-borne bacterial species in the far shore of the East China Sea is the lowest with only 406 species. The main dominant groups are Proteobacteria and Bacteroidetes, of which the Proteobacteria dominates. Pseudoalteromonas is an absolute dominant genus of γ-Proteobacteria, distributed in ballast water samples of various sea areas and has a certain positive correlation with temperature and nutrients but strong negative correleation with salinity and pH; Cyanobacteria and Planctomycetes are the dominant phyla detected in ballast water samples exchanged in the distant shores of the South China Sea, much higher than those in other sea areas, and their corresponding originals. There was a significant positive correlation between dissolved oxygen and environmental factors in the genera Chlorophycoccus and Pseudomonas; it was negatively correlated with temperature and nutrients; and Salinimicrobium was the unique genus which is the dominant phytoplankton in the ballast water samples from the Yellow Sea. Dissolved oxygen and pH were positively correlated with this genus which is negatively correlated with nutrient salts. Marine microorganisms in different sea areas and their marine environment determined the impact on the diversity of ballast water microbes and the unique environment of ballast tanks has certain choices for ballast water microbes. The role of exchanging ballast water on the open seas in accordance with the IMO guidelines has a great influence on the compositional structure of the ballast water microbial community. Therefore, it plays an important role in the protection of the marine environment and the prevention of biological invasion and spread of pathogenic bacteria.