This study aimed to investigate the differential responses of rhizosphere and bulk soil microbial diversity to long-term fertilization and to identify the key nutrient drivers. 【Method】 Rhizosphere and bulk soils were collected from tobacco plants under five treatments in a long-term field experiment established in 2010. The samples were collected from plots with no fertilization (CK), inorganic fertilizer alone (NPK), organic fertilizer alone (OM), combined inorganic and organic fertilization (NPKO), and inorganic fertilizer plus green manure incorporation (NPKG). Using high-throughput sequencing, soil physicochemical analyses, and functional prediction, we evaluated the effects of different fertilization treatments on the composition, diversity, and potential functions of bacterial and fungal communities in rhizosphere and bulk soils. 【Result】 The results showed that long-term fertilization significantly altered bacterial community structure in both rhizosphere and bulk soil, whereas fungal community structure responded significantly only in bulk soil. Proteobacteria, Actinobacteriota, Acidobacteriota, Ascomycota, and Basidiomycota were the dominant phyla shared by both habitats. Fertilization generally promoted the enrichment of Sphingomonas. Meanwhile, compared with CK, the relative abundance of Fusarium under NPKG increased significantly by 117.20%, whereas NPKO increased the abundance of Humicola in the rhizosphere and reduced Fusarium to the lowest level among all treatments, representing a 42.86% decrease relative to CK. Also, fertilization significantly increased soil carbon (32.32%–159.76%) and nitrogen (17.68%–229.80%) fractions. Soil pH, total nitrogen, total organic carbon, and dissolved organic carbon were the key factors driving rhizosphere bacterial succession (P < 0.05), whereas bulk soil fungal communities were mainly driven by alkali-hydrolyzable nitrogen. Fertilization enhanced the potential functions of bulk soil bacteria related to carbon and nitrogen metabolism and transmembrane transport. In addition, NPKO not only strengthened the potential of fungi to decompose complex organic substrates, but also reduced the predicted abundance of functions associated with potential rhizosphere pathogens.【Conclusion】 Bacterial and fungal communities showed clear habitat-specific responses to long-term fertilization, with their succession driven primarily by multiple nutrient factors in the rhizosphere soil and by alkaline hydrolyzable nitrogen in bulk soil. Additionally, combined organic–inorganic fertilization was more effective in coordinating nutrient turnover and maintaining rhizosphere microecological health.