Medicinal herbs have been increasingly used for therapeutic purposes against a diverse range of human diseases worldwide. However, inevitable contaminants, including mycotoxins, in medicinal herbs can cause serious problems for humans despite their health benefits. The increasing consumption of medicinal plants has made their use a public health problem due to the lack of effective surveillance of the use, efficacy, toxicity, and quality of these natural products. is commonly utilized in traditional Chinese medicine and is susceptible to contamination with mycotoxins. Here, we evaluated the mycotoxins, mycobiota and toxigenic fungi in the traditional medicine . A total of 28 out of 63 sample batches (44.4%) were found to contain mycotoxins. Among the positive samples, the contamination levels of AFB, AFG, AFG, and OTA in the positive samples ranged from 0.52 to 32.13 μg/kg, 5.14 to 20.05 μg/kg, 1.52 to 2.33 μg/kg, and 1.81 to 19.43 μg/kg respectively, while the concentrations of ZEN and T-2 were found to range from 2.85 to 6.33 μg/kg and from 2.03 to 2.53 μg/kg, respectively. More than 60% of the contaminated samples were combined with multiple mycotoxins. Fungal diversity and community were altered in the contaminated with various mycotoxins. The abundance of and increased in the contaminated with aflatoxins (AFs) and ZEN. A total of 95 strains of potentially toxigenic fungi were isolated from the samples contaminated with mycotoxins, predominantly comprising (73.7%), (20.0%), and (6.3%). Through morphological identification, molecular identification, mycotoxin synthase gene identification and toxin production verification, we confirmed that AFB and AFG primarily derive from , OTA primarily derives from , ZEN primarily derives from , and T-2 primarily derives from in . These data can facilitate our comprehension of prevalent toxigenic fungal species and contamination levels in Chinese herbal medicine, thereby aiding the establishment of effective strategies for prevention, control, and degradation to mitigate the presence of fungi and mycotoxins in Chinese herbal medicine.