Codonopsis pilosula is an important Chinese herbal medicine. However, fresh C. pilosula is prone to decay during storage due to microorganism infections, seriously affecting the medicinal value and even causing mycotoxin accumulation. Therefore, it is necessary to study the pathogens present and develop efficient control strategies to mitigate their detrimental effects on the herbs during storage. In this study, fresh C. pilosula was collected from Min County in Gansu Province, China. The natural disease symptoms were observed during different storage stages, and the pathogens causing C. pilosula postharvest decay were isolated from the infected fresh C. pilosula. Morphological and molecular identification were performed, and pathogenicity was tested using Koch’s postulates. In addition, the control of ozone was examined against the isolates and mycotoxin accumulation. The results indicated that the naturally occurring symptom increased progressively with the extension of storage time. The mucor rot caused by Mucor was first observed on day 7, followed by root rot caused by Fusarium on day 14. Blue mold disease caused by Penicillum expansum was detected as the most serious postharvest disease on day 28. Pink rot disease caused by Trichothecium roseum was observed on day 56. Moreover, ozone treatment significantly decreased the development of postharvest disease and inhibited the accumulations of patulin, deoxynivalenol, 15-Acetyl-deoxynivalenol, and HT-2 toxin.