The root of Angelica sinensis (Oliv.) Diels (Ang) is a bulk Chinese herbal medicine, and the microecological regulation is a sustainable means to enhance its quality. In this study, Angs at five bases (LZ, XZ, QS, PM, MZC) in Minxian County, Gansu Province were taken as the research objects. These bases locate in the typical spatial spans of the Ang authentic area, and are important planting bases. The Angs from production bases were systematically compared with respect to soil physicochemical properties, rhizosphere fungi, endophytic fungi, and metabolic profiles. Typically, LZ showed low levels of available nitrogen (AN), available phosphorus (AP), available potassium (AK), and soil enzyme activities, while QS had the highest AN, AP, AK, and cellulase activity. Although XZ exhibits moderate nutrient contents, its sucrase activity was highest. Based on microbiome sequencing, rhizosphere fungal communities responded these physicochemical differences, with XZ harboring more probiotics, including Tetracladium, Itersonilia, and Vishniacozyma, compared to LZ, which showed the lowest abundance of these microorganisms. Differential patterns were presented among their endophytic fungal communities. Through LC-MS detection, it was revealed that Angs in QS synthesized more short peptides, organic acids and phenylpropanoid ingredients. Upregulated metabolites with plant defense efficacy are mostly found in LZ's Angs. Whereas XZ's Angs had a moderate abundance of bioactive ingredients. Structural equation fitting further highlighted the synergistic effects of soil nutrients (AN, AP, AK) with key fungal genera (Tetracladium, Itersonilia, Paecilomyces, Aspergillus) and their potential shaping effects on amino acids, short peptides, organic acids, and phenylpropanoids such as L-phenylalanine, acetyl-L-tyrosine, Ile-His-Met-Thr, caffeic aldehyde, Lpipecolic acid, and 4-methoxycinnamic acid. This study further refined the potential action modes of these key microecological factors shaping the accumulation of main types of active ingredients. These results are expected to provide an important reference for the development of quality regulation strategies in Ang ecological cultivation.
