Abstract: In order to understand the changes of fungal community and metabolites in mildew Liupao tea, the fungal diversity of mildew Liupao tea samples (GGZ) and normal Liupao tea samples stored in bamboo basket (BDL) were analyzed by Illumina high-throughput sequencing technology, and ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to analyze the metabolites in these samples. Further, pathway enrichment analysis was performed on the significantly differential metabolites, and the correlation between the differential metabolites and the differential microorganisms was calculated. The results showed that the most abundant fungi in mildew Liupao tea were Ascomycota and Basidiomycota in phylum level, Aspergillus and Wallemia in genus level. Aspergillus and Penicillium belonging to Ascomycota were more abundant in BDL. Two of the dominant fungi related to mildew in Liupao tea, A. Ruber and W. sebi, showed significantly (P<0.05) higher abundance in GGZ than in BDL. In addition, higher contents of flavonoids along with the changing amino acids metabolism and down-regultated caffeine metabolism was observed in mildew Liupao tea. In mildew Liupao tea, the content of 2-hydroxy-isocaproic acid with certain cytotoxicity and genotoxicity was up-regulated and negatively correlated with reduced abundance of Penicillium. These data unveiled that A. ruber, W. sebi and 2-hydroxyisocaproic acid were potential risk factors in food safety assessment of Liupao tea, and the changes of flavonoid content, amino acid metabolism and caffeine metabolism in mildew Liupao tea might be related to quality changes.