Traditional Chinese medicines (TCM) infected with toxigenic fungi have become an increasingly outstanding problem for human health. The existing reports mainly focused on the detection methods of mycotoxins in TCMs, however, the effect of mycotoxin production on the inherent quality of TCMs has not been investigated and elucidated so far. In this study, sterilized Glycyrrhiza uralensis was inoculated and incubated with Aspergillus carbonarius for some days to investigate the effect of ochratoxin A (OTA) accumulation on the inherent quality of G. uralensis by determining the content changes of OTA and five active components (liquiritin apioside, liquiritin, liquiritigenin, glycyrrhizic acid, and glycyrrhetinic acid). The results showed that consecutive incubation of G. uralensis with A. carbonarius within 30 days led to the production and accumulation of OTA, and the content reduction of five active components. A negative correlation was illustrated between the contents of OTA and active components.