| Root rot is one of the major diseases in the cultivation of Bupleurum chinense DC., severely constraining the development of the industry. In this study, high-throughput sequencing was employed to systematically analyze the fungal and bacterial community structures, temporal variations, and functional profiles of key differential taxa in bulk soil, rhizosphere soil, and the root endosphere across healthy plants, early-stage infected plants, and late-stage infected plants. The results showed that root rot predominantly affected the microbial communities in the root endosphere. As the disease progressed, fungal diversity in the root endosphere declined sharply, with a significant enrichment of Fusarium, Haematonectria, Volutella, and Cylindrocarpon. Notably, Fusarium solani was highly enriched in root at the late-stage infection, suggesting it may be the primary causal agent of root rot in B. chinense. In contrast, bacterial diversity in the root endosphere increased with disease development, accompanied by a notable rise in the relative abundance of the Allorhizobium–Neorhizobium–Pararhizobium–Rhizobium, implying that B. chinense may recruit beneficial microbes as part of a defense strategy to enhance resistance to root rot disease infection. This study provides critical insights for screening pathogenic fungi and beneficial antagonistic microbes associated with B. chinense root rot. |