A method for simultaneous determination of 12 mycotoxins in Pericarpium Citri Reticulataeby HPLC-MS/MS was established to analyze the residues of mycotoxins, inwhich from Three Gorges Reservoir area of China, including AFB1, AFB2, AFG1, AFG2, T-2, FB1, FB2, FB3, ZEN, OTA, OTB and DON.In addition, a probabilistic assessment model based on Monte Carlo simulation method was established in combination with pollution data, and the health risk assessment was carried out by the exposure limit method (MOE).The results showed that the method with strong specificity, good linearity and accurate recovery was established and could be used for the determination of 12 mycotoxins in Pericarpium Citri Reticulatae.In general, the total pollution rate of different degrees of pollution in the 36 batches of Pericarpium Citri Reticulatae sampleswas 75 %. It should be noted thatthe proportion of positive samplescontaminated by one toxin was the highest (59.26 %), and the detection rate of FB3 in Pericarpium Citri Reticulataewas the highest (66.67%), followed by AFG1 (44.44 %), indicating that the medicinal material polluted by AFG1 and AFB3 alone or simultaneously was more serious. Specifically, the detection rate of mycotoxins in Chongqing was the highest (92.31%) on account of the high temperature and humidity in Chongqing, followed by Southeast of Sichuan (83.33%) and West of Hubei (45.45%).On the other hand, the MOE of AFB1 and AFB2 calculated were both greater than 10000, indicating that the health risk of AFB1 and AFB2 exposure caused by taking Pericarpium Citri Reticulatae was low, but the risk of high intake population was higher than that of conventional intake population, which needed to be paid attention to. This study can provide a reference for the safety assessment of clinical medication of Pericarpium Citri Reticulatae inThree Gorges Reservoir area.