The fungus Penicillium citrinum (P. citrinum), which is found in Chinese dark tea, is involved in the production of citrinin (CIT), a secondary metabolite with renal toxicity. In this study, a rapid method was used to detect CIT in Chinese dark tea samples from different regions and years. Of the 216 samples tested, 5 were detected to have CIT contamination, with a concentration ranging from 272.43±16.57 to 649.68±62.16 μg·kg-1. Risk assessment for consuming dark tea showed that four heavy intake consumer groups in the deterministic risk assessment had hazard quotients (HQ)> 1, and the HQ for the probabilistic risk assessment was significantly below the acceptable level of 1.0. Furthermore, we found that tea polyphenols (TPs) inhibited the growth of P.citrinum. Transcriptome results showed that there were 483 downregulated and 783 upregulated genes between the TPs and control groups. Of which, orf1 and ctnD were significantly downregulated, demonstrating that TPs can affect CIT biosynthesis. Our research indicates that CIT in dark tea is within an acceptable risk level, and provides new insights into the inhibition of CIT. Furthermore, this study suggests that the suppression of CIT in dark tea by polyphenols make the consumption of dark tea safe.