Angelica sinensis, a well-known medicinal herb in demand worldwide, is mainly cultivated in a cool high-altitude mountainous region in northwest China. Recently, due to climate change and the excessive use of chemical fertilizers, soil borne diseases are leading to severe production losses of A. sinensis. Here we developed a novel attapulgite coated with a particular biocontrol agent (APBA) and tested its efficacy for disease control of Fusarium root rot in A. sinensis. The plate confrontation experiment showed the biocontrol bacterium significant inhibited a variety of pathogenic fungi causing root rot. Five treatments were then evaluated in the field experiment: empty attapulgite carrier (AP), chemical fertilizer (CF), and organic fertilizer (OF) with or without the AP-coated biocontrol agent, respectively. These field trials demonstrated the incidence of Fusarium root rot disease was significantly reduced from 30.56% (CF) to 12.4% when the CF was combined with APBA (BICF), reaching as low as 11% when the OF was combined with APBA (BIOF). In the rhizosphere microbial community, bacterial diversity was significantly higher under the BICF than CF treatment, whereas the fungal diversity was lower in the BIOF treatment. Furthermore, the structure of both soil bacterial and fungal communities was considerably changed when APBA was applied, irrespective of its combination with CF or OF. Specifically, APBA enriched the relative abundances of beneficial genera, such as Bryobacter, Sphingomonas, Rokubacteria and (among others), whereas it diminished those of Gibberella, Fusarium, Cylindrocarpon, and Plectosphaerella which were positively correlated with the rot disease index. Redundancy analysis and Pearson correlations revealed that, besides their significant positive relationships with soil total carbon (TOC), total nitrogen (TON), organic matter (OM), total potassium (TK) and ammonium nitrogen (NH₄-N), the APBA treatments for OF and CF were both dominated by Acidobacteria, Chloroflexi, Gemmatimonadetes, Actinobacteria, Rokubacteria, and Nitrospirae. Our PICRUSt functional data prediction indicated that APBA's application significantly affects the functioning of the rhizosphere's microbial community, but with more signal pathways and functions found overrepresented in the BIOF and BICF treatments. This comprehensive study suggests the application of this novel biocontrol agent can effectively suppress the incidence of root rot disease in A. sinensis, by improving soil chemical properties and altering microbial community composition in the A. sinensis rhizosphere.