Characterizing soil bacterial community is important to understand microbial distribution affected by environmental factors. Here, we investigated the bacterial communities distributed from different location on Nanshazhou island, South China Sea. We collected and compared soil bacterial communities from central island, intertidal island, and inshore island. Results showed no difference in the bacterial richness and diversity for the soils from the three different locations. However, weighted and unweighted UniFrac distances analysis revealed that the three soil samples were clearly separated from each other. Five bacterial phyla, including Proteobacteria, Bacteroidetes, Verrucomicrobia, Spirochaetes and Tenericutes were more abundant in the inshore island sample; while Deinococcus-Thermus was more abundant in the intertidal island sample; and the central island sample had more abundant Gemmatimonadetes and Planctomycetes. Bacterial structure showed significantly positive relationships with organic matter content, but it was significantly negatively correlated with sodium content. Furthermore, a network analysis based on Spearman correlation coefficients showed that there were similar numbers of positive and negative correlations within the bacterial community of Nanshazhou island. Our results revealed that the soil bacterial communities in the three sampling sites were easily affected by environmental fluctuations.