Salvia miltiorrhiza Bunge, a staple in Chinese herbal medicine, is widely used for the treatment of cardiovascular diseases. However, the yield and quality of S. miltiorrhiza have decreased dramatically because of severe continuous cropping obstacles stemming from inadequate wild resources and limited genuine production areas. The rhizosphere soil samples of S. miltiorrhiza under three cropping modes-rotation cropping monoculture (RCMO), continuous cropping monoculture (CCMO), and intercropping mix-culture (ICMI)-were collected from the city of Bozhou in the Anhui province. The MiSeq high-throughput sequencing technique, targeting the V3-V4 region of the bacterial 16S rDNA gene and the V4 region of the fungi 18S rDNA gene, was used to investigate the bacterial and fungi community structure and analyze the links between the microbial community structure and soil environmental parameters. The goal of this study was to illuminate the mechanism of continuous cropping obstacles that occur in S. miltiorrhiza from the perspective of a rhizospheric micro-ecological environment. Overall, most Alpha diversity indexes of microbial communities followed the order of RCMO > ICMI > CCMO, but significant differences were not observed between the three cropping modes. The Shannon-Wiener index of bacterial community and the mycorrhizal colonization of S. miltiorrhiza under RCMO were higher than those under CCMO. The relative abundance of the top 10 dominant bacterial phyla accounted for 94%, and all of the 10 dominant phyla were the same across all cropping modes; these were Proteobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, Actinobacteria, Bacteroidetes, Verrucomicrobia, Unclassified, Firmicutes, and Chloroflexi phyla. In terms of bacterial community composition, the relative abundance of Gemmatimonadetes phylum under RCMO was lower than that under CCMO and ICMI. In contrast, the dominance of Planctomycetes and Bacteroidetes phyla under RCMO and ICMI were higher than that under CCMO. In total, only nine fungi phyla were found in this study, most of them unclassified fungi. The relative abundance of Zygomycota, Chytridiomycota, and Ascomycota phyla under RCMO and ICMI increased compared to CCMO. Furthermore, the relationship between the microbes differed significantly across the three cropping modes. The rotation of S. miltiorrhiza even reversed the relationship between fungi, from negative undehttp://toutiao.7junshi.com/?qid=minitopr CCMO to positive. The ratio of beneficial Bacillus genus decreased but pathogenic Fusarium genus increased under CCMO, which might change the relationship between the microbial community and dramatically exacerbate the diseases of S. miltiorrhiza. Differentiations between the microbial communities were not evident between the three cropping modes according to principal coordinates analysis (PCoA). The variation in microbial communities was controlled by eight principal coordinates, among which the first two principal coordinates explained less than 30% of the total variance. This indicates that there was no dominant factor that shaped the microbial community. The results showed that soil pH, ORP, and partial mineral nutrients were improved under RCMO and ICMI modes compared to CCMO. A Monte Carlo permutation test revealed that soil environmental parameters were closely related to the differences in the bacterial community but not the fungi community. Total and available K were positively correlated to bacterial and fungi communities under ICMI, respectively. In contrast, fungi communities under RCMO and CCMO were better adapted to low available K and high ORP in soil environments. Our study indicated that RCMO and ICMI can, to some extent, improve the physicochemical properties of soil, increase the diversity of microbial community in the rhizosphere soil of S. miltiorrhiza, and change the microbe-microbe and microbe-plant relationships in comparison with CCMO, thus alleviating the continuous cropping obstacles.