Organic fertilizers produced from agricultural waste materials using earthworms have many advantages. The impact of vermicompost bio-organic fertilizer (VcF) prepared from waste mushroom bran on the quality of Chinese herbal medicine and soil health deserves attention. We conducted a field experiment to explore the quality of Rhizoma atractylodis and soil, using chemical fertilizer and VcF at dosages of 30 t·ha−1 and 40 t·ha−1. The results demonstrated that VcF significantly increased the contents of atractylenolide II, β-eudesmol, atractylenol, and atractylenolone by 34%, 175%, 72%, and 24%, respectively, along with a 70% increase in yield compared to the control. VcF significantly increased the available phosphorus content and the activity of the soil enzymes (α-Galactosidase, β-Galactosidase, and peroxidase), while reducing the nitrate nitrogen content. The addition of vermicompost did not change the soil bacterial diversity, while it significantly increased the soil fungal diversity. VcF improved the soil fungal diversity and significantly enhanced the relative abundance of the bacterial phylum Actinobacteriota and WPS-2, as well as the fungal phylum Ascomycota. Vermicompost significantly increased the relative abundance of bacteria phylum Actinobacteriota and WPS-2, as well as the fungi phylum Ascomycota. Actinobacteria mainly participate in the decomposition of detritus and the heterotrophic nutrient cycle. A Principal Coordinates Analysis of the soil bacterial and fungi communities suggested a significant impact of vermicompost application on the community structure of the soil bacteria. Conversely, no significant variance was detected in the bacterial community composition across the two levels of vermicompost. This study contributes to the enhancement of fertilization strategies for Atractylodes macrocephala, broadens the application scope of vermicompost, and advances the growth of organic agriculture.
