【Objective】 Salvia miltiorrhiza Bunge, commonly known as Danshen, is a perennial herbaceous plant that is a traditional and widely used medicinal herb in China. Intensive cultivation has led to frequent outbreaks of soil-borne diseases, notably root rot, which significantly limits the yield and quality of Danshen. 【Method】 This study compared the antagonistic abilities of four Lysobacter strains isolated from the rhizosphere of Solidago canadensis against the root rot pathogen Fusarium oxysporum 220. To identify the most efficient fermentation substrate for the selected strain, microbial solid-state fermentation was conducted using tobacco stalk, rice straw, sorghum straw, corn straw, and Solidago canadensis straw. Based on the optimal fermentation substrate, a bio-organic fertilizer(BOF) was prepared. Subsequently, pot experiments were conducted to evaluate the effectiveness of this BOF in controlling Danshen root rot. Finally, based on metagenomic sequencing, the key microbial groups and functional genes enriched by BOF were analyzed. 【Result】 The results of the study demonstrated that the Lysobacter enzymogenes strain Le395 exhibited strong antagonistic effects against the root rot pathogen F. oxysporum 220. In the organic fertilizer raw material screening experiment, it was found that the optimal fermentation substrate for strain Le395 was Solidago canadensis straw. In the pot experiment, it was observed that the application of the BOF effectively controlled Danshe root rot disease. Compared to the control group(CK), the disease incidence was reduced by 50.3%, and the disease index decreased by 50.2%. Additionally, the BOF showed significant growth-promoting effects. The above-ground fresh biomass of the plants treated with BOF increased by 163.1%, while the below-ground fresh biomass increased by 147.0% compared to the CK group. Finally, qPCR and metagenomics sequencing analyses revealed that the application of Le395 BOF significantly decreased the abundance of Fusarium and F. oxysporum in the rhizosphere of Danshen. It also increased the abundance of Lysobacter and L. enzymogenes, while modulating the rhizosphere microbial community structure and enhancing the abundance of disease resistance- and growth promotion-related functional genes in the rhizosphere. 【Conclusion】 These findings provide a theoretical and technical foundation for developing an ecological and sustainable strategy for controlling Danshen root rot using bio-organic fertilizer.