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Objective To elucidate the natural occurrence of multi-mycotoxin in commercial loose-packed rice from Yunnan Province in 2019. Methods A total of 90 rice samples collected from 11 cities in Yunan Province were analyzed for 16 kinds of mycontoxin by ultra perfermance liquid chromatography-tandem mass spectrometry. Results Among the 90 rice samples, the detection rate of aflatoxin B1(AFB1) was 13. 33%(12/90), exceeding the 10 μg/kg stipulated by the national food safety standard GB 2761-2017 for the limit of mycotoxin in food, and the exceeded rate was 10.00% (9/90). Other mycotoxins did not exceed the limit. Conclusion The commercial loose-packed rice samples in Yunnan Province were contaminated by multi-mycotoxins in this study, but the levels of contamination were low.