Widely targeted metabonomics and high-throughput sequencing technologies were used to investigate the effects of coexisting microorganisms on secondary metabolites in Pericarpium Citri Reticulatae ‘Chachiensis’ (PCRC),which will provide a scientific basis for the aging mechanism of PCRC.A Waters ACQUITY UPLC HSS T3 C₁₈ column (1.8 μm,2.1 mm×100 mm) was used with 0.04% acetic acid-acetonitrile gradient elution as mobile phase at a flow rate of 0.4 mL/min.Electrospray ionization was selected for collection and detection in positive and negative ion modes.DNA was extracted from oral swab samples by CTAB method,and library construction kit was used for library construction.The library was quantified by Qubit and Q-PCR,and sequenced by HiSeq 2500 PE250.Correlation analysis was conducted between the differential metabolites and the differential microorganisms.The results showed that 386 kinds of secondary metabolites were identified,including 79 phenolic acids,143 flavonoids,4 anthraquinones,17 lignans and coumarins,3 tannins,47 alkaloids,6 terpenoids and 87 other kinds.Principal component analysis and heatmap analysis showed that the contents of secondary metabolites in the samples stored for 1 year and 3 years were significantly different.A total of 58 genera were obtained by comparing the gene sequences of high-throughput sequencing with the microbial reference database.The bacterial colonies of the samples stored for 1 year and 3 years were similar in structure,but the relative abundance was different from that of the dominant genus.The correlation analysis of differential metabolites and differential microorganisms showed that the dominant fungi,such as Penicillium and Aspergillus could significantly affect the content of flavonoids and aromatic compounds.The aging mechanisms may be closely related to the change of active components and aroma components affected by the coexisting microorganisms.