Samples of Pericarpium Citri Reticulatae (Citrus reticulata 'Chachi', CP-‘Chachi’), which collected in December of 2017, 2013, 2003 and 1993 with the natural aging process for 5, 10, 20 and 30 years, were used to compared the changes in total polyphenols, total flavonoids and fungal community composition. The relationship among these factors was analyzed. The content of flavonoids in CP-‘Chachi’ was qualitatively and quantitatively determined by HPLC system. ITS (Internal Transcribed spacer) sequencing techniques were used to detect the changes of microbial communities during the aging process of CP-‘Chachi’. The results indicated that the levels of flavonoids and total polyphenols, except for hesperidin, increased aging time, with the most significant growth observed in 5-O-desmethyl nobiletin at 298.36%, while hesperidin decreased by 32.52%. The three most abundant genera were Xeromyces, Symmetrospora and Cladosporium, and the highest number of genera was found in CP-2013. The community composition of CP-1993 and CP-2003 was highly similar, Xeromyces accounted for 84.04% and 83.58% in CP-1993 and CP-2003, respectively. The findings demonstrated that only the abundance of Xeromyces was positively correlated with the accumulation of active components during the aging process of CP-‘Chachi’. This indicated that Xeromyces was considered the dominant genus responsible for the aging quality of CP-'Chachi'. The relationship between the changes in flavonoids and fungal diveresity was preliminarily verified, which provided new insights into the study of the aging mechanism of CP-‘Chachi’ and its influencing factors on quality.