In this study, the changes in soil bacterial community structure, quantity and function were examined by a 3 a fertilization experiment using quantitative PCR and high-throughput sequencing techniques, which included three treatments:organic fertilizer (YJ), inorganic fertilizer (WJ), and the combined application of organic and inorganic fertilizer (YW). The results showed fertilization treatments caused the changes in soil physiochemical properties, specifically, WJ and YJ decreased soil pH, YJ significantly increased soil organic matter content, YW increased available nutrients and soil organic matter content while maintaining soil pH. Additionally, the quantity, community structure and function of soil bacteria also changed, the copy numbers of bacteria 16S rRNA gene in YJ and YW soils were significantly higher than in WJ soil, the alpha diversity of soil bacteria community in YW soil was the highest. Principal coordinate analysis and ANOSIM test further revealed soil pH had greatest influence on soil bacterial community structure. Moreover, some bacterial groups were obviously enriched, YW soil had significantly higher abundances of plant growth-promoting bacteria such as Gemmatimonadaceae, Micrococcaceae and Haliangiaceae. YJ soil had higher abundance of bacteria with nitrogen fixation or biocontrol functions such as Intrasporangiaceae, Xanthomonadaceae, Chitinophagaceae and Burkholderiaceae. Furthermore, YW and YJ increased the abundance of nitrogen-fixing bacteria Rhizobiaceae. Notably, the change in bacterial community structure may further influence bacterial community function, especially, YW can greatly enhance nitrification function of bacterial community. The above findings provide a scientific basis for rational fertilization in tobacco production.