Chuan chenpi is obtained by aging the peel of Citrus reticulata cv. ‘Dahongpao’, a traditional Chinese citrus variety. Chenpi has been used in traditional Chinese medicine since ancient times. It is believed that the longer the ripening period, the better the health properties. The composition of the metabolome of Chuan chenpi and how different aging periods affect it are not known. Current analysis was performed using Chuan chenpi aged for one (CR1), five (CR5) and ten (CR10) years. Initially, the total flavonoid and phenolic content were quantified, and then the global metabolomic profiles of CR1, CR5 and CR10 were studied. The total flavonoid and phenolic content increased significantly in CR5 compared to CR1 and then decreased in CR10. The metabolomic analyses led to the identification of 781 compounds belonging to more than 19 classes. Flavonoids and phenolic acids accounted for almost half (~48%) of the Chuan chenpi metabolome. Other major classes included amino acids (~8%), alkaloids (7.17%), organic acids (~7%), sugars (5.5%), nucleotides and derivatives (~5%), free fatty acids (3.33%) and other classes. The metabolite diversity of glycerol esters, terpenoids and stilbenes was constant during the three storage periods, whereas those of lignans, vitamins, coumarins, lipids and free fatty acids showed slight variations. The subclass distribution of phenylpropanoids, quinones, sphingolipids, and organic acids showed a decrease in diversity from CR1 to CR5, with CR10 showing a further decrease or remaining constant. Amino acids and derivatives, phenolic acids and flavonoids showed an increasing trend in the number of metabolites over the storage period. Compared to CR5, CR10 showed a higher number of differentially accumulated metabolites; in particular, flavonoids, phenolic acids and organic acids showed increased accumulation in CR10. In conclusion, the metabolome of Chuan chenpi is rich in flavonoids and phenols. Aging significantly affects the metabolome composition. Both CR5 and CR10 may be useful materials for health studies depending on the objectives of pharmacological use.