Angelica sinensis, a Chinese herbal medicine, is susceptible to molds during storage, reducing its quality, and even generating mycotoxins with toxic effects on human health. Fresh A. sinensis was harvested from Min County of Gansu Province in China and kept at room temperature. Naturally occurring symptoms were observed during different storage stages. Molds were isolated and identified from the diseased A. sinensis using morphological and molecular biology methods. The impact of ozone treatment on postharvest disease development and mycotoxin production was investigated. The results indicated that A. sinensis decay began on day 7 of storage and progressed thereafter. Nine mold species were isolated and characterized: day 7, two Mucormycetes; day 14, Clonostachys rosea; day 21, two Penicillium species and Aspergillus versicolor; day 28, Alternaria alternata and Trichoderma atroviride; and day 49, Fusarium solani. Ozone treatment markedly inhibited the development of postharvest disease and the mycotoxin production (such as, patulin, 15-acetyl-deoxynivalenol, and sterigmatocystin) in the rotten tissue of A. sinensis inoculated with the nine isolates.