Soil microbial characteristics can sensitively reflect soil quality and health. In order to illustrate the difference among various ecological regions in microbial information, the microbial community structures in tobacco-planted soil were assessed and analyzed by high throughput sequencing (16S V4 region). The operational taxonomic units (OTUs) were significantly diverse in different ecological regions. The soil microbial population in the west of Guizhou Province was relatively higher than that in the east of Guizhou, while that in the south was higher than that in the north. The microbial phyla Proteobacteria and Actinobacteria were the top two in relative abundance in the north of Guizhou Province. In central Guizhou Province, Proteobacteria abundance was significantly greater than Actinobacteria abundance. The soil dominant genera in the southwest and central Guizhou Province were much more than other regions. However, the microbial population was imbalanced, inducing potential outbreak of soil-borne disease. This study provides a better understanding of the soil microbial community and will also provide a theoretical basis to build a good foundation for soil bio-remediation in the future.