Citri Reticulatae Pericarpium is made from the dried peel of Citrus reticulata Blanco and its cultivated varieties, of which the one made from Citrus reticulata ‘Chachiensis’ is Guangchenpi, a widely known traditional Chinese medicine. This study explores the effects of drying and aging on the metabolic quality of Guangchenpi and identifies potential medicinal active substances in Guangchenpi through gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry/mass spectrometry combined with network pharmacology analysis. Six types of primary metabolites and 518 types of phenylpropanoid metabolites were identified in peels of Citrus reticulata ‘Chachiensis’ and Guangchenpi samples, among which 28 were key active ingredients in traditional Chinese medicine (such as quercetin-7-O-rutinoside and 3′,4,7-trihydroxyflavone), and 34 phenylpropane metabolites(such as esculin and imperatorin) are major pharmacologically active ingredients. After drying, the contents of 169 substances were significantly up-regulated. During the aging process, the variety of metabolites increased, and the content of metabolites such as flavonoid-C-glucoside and 3′,4,7-trihydroxyflavone significantly increased with the prolonged aging time. Chemical modifications of bioactive components also accompanied the drying and aging process. After drying, glucoside degradation and rhamnoside synthesis of various flavonoids in Guangchenpi occurred, whereas the aging process was dominated by oxymethylation. This study helps understand the aging mechanism of Guangchenpi and the phenomenon of ‘Extra aging makes for better Chenpi’. It also provides theoretical support for the efficient development and utilization of Guangchenpi.