SummaryIn this study, a full factorial design with three temperature levels (20, 30 and 40 °C), three moisture content (MC) levels (8%, 15% and 22%), and four storage times (7, 14, 21 and 28 days) was used to investigate the changes of aflatoxins (AFs), active constituents, and antioxidant activities in Hangbaiju (HBJ, Chrysanthemum morifolium) after simulated inoculation with Aspergillus parasiticus. The results showed that AFs could be produced in the range of 20~30 °C and 8~22% MC after mould infection, but both mould growth and AFs production were inhibited under the tested MC condition at 40 °C. The analysis of variance (anova) indicated that the temperature, time, interaction between the temperature and time, and interaction between MC and time had significant effects on the total aflatoxins (AFTOT) accumulation. Under 20 and 30 °C, AFTOT in inoculated HBJ usually increased with the increase of MC and storage time, while its active constituents and antioxidant activities decreased with the increase of AFTOT under corresponding storage conditions. Pearson correlation analysis suggested that relatively stronger negative correlations were observed between luteolin‐7‐O‐glucoside (LUT7G), total phenolic content (TPC), total flavonoid content (TFC), and AFTOT. Grey correlation analysis (GCA) showed that antioxidant activity was highly linked to the content of active constituents, and the characteristic flavonoid LUT7G exhibited the highest grey correlation degrees (GCDs) in the three antioxidant activities. The AFTOT reached the highest level (31.15 μg kg−1) after 28 days of storage at 30 °C and 22% MC; meanwhile, LUT7G, TPC and TFC decreased by 93.66%, 20.77% and 55.50%, respectively, and all the three antioxidant activities indicated more than 25% reduction. This is the first study about the changes and relationships of AFTOT, active constituents and bioactivities in the medicinal food influenced by A. parasiticus under different storage conditions. These results provide important references to prevent AFs production and quality control for HBJ and other medicinal foods influenced by A. parasiticus in storage strategy.