This study aimed to clarify the effects of different fertilization regimes on bacterial community structure and intraspecific interactions in rhizosphere soil of Scutellaria baicalensis Georgi，and further lay the foundation for future research of reasonable fertilization of Scutellaria baicalensis Georgi and improving soil microbial diversity. The high-throughput sequencing technology was employed to compare the bacterial community structure among soils that subjected to three fertilization regimes:non-fertilization control (CK)，chemical fertilizer application only (NPK)，and chemical fertilizer application combined with bio-organic fertilizer (NPKM). Compared with CK and NPK treatments，the bacterial richness was significantly increased by 11.51% and 7.37% under NPKM treatment，respectively. NPK and NPKM significantly affected the bacterial community structure as compared with CK. Proteobacteria was the most abundant phylum because of the highest relative abundance (>28%)in different treatments. The dominant species in CK belonged to Acidobacteria，which is oligotrophic microbes. The indicator species in NPK were Proteobacteria and Bacteroides，which favor the eutrophic environments. NPKM stimulated the abundance of Actinobacteriota and Chloroflexi，which play important roles in the decomposition of recalcitrant organic matters. The co-occurrence network analysis demonstrated that bacteria mainly showed cooperative relationships，as the positive correlation was 64.32% . Compared with NPK treatment，the number of the nodes in CK and NPKM were significantly increased by 4.76% and 5.95%，respectively，while the number of the edges in CK and NPKM were significantly increased by 12.13% and 10.54%，respectively. These results indicating that only applying chemical fertilizer would hinder the improvement of connection between bacteria and system stability. Our results indicated that chemical fertilizer application，especially chemical fertilizer application combined with bio-organic fertilizer，could provide a more suitable environment for Scutellaria baicalensis Georgi by enhancing the interaction between soil microbes，optimizing bacterial community composition.