Flavonoids are essential substances with antioxidant properties and high medicinal value. Citrus reticulata ‘Chachi’ peel (CRCP) is rich in flavonoids and has numerous health benefits. The different maturity periods of CRCP can affect the flavonoid contents and pharmacological effects. In this study, we successfully performed UPLC-ESI-MS/MS-based metabolic analysis to compare the metabolites of CRCP at different harvesting periods (Jul, Aug, Sep, Oct, Nov, and Dec) using a systematic approach. The results revealed the identification of a total of 168 flavonoid metabolites, including 61 flavones, 54 flavonols, 14 flavone C-glycosides, 14 dihydroflavones, 9 flavanones, 8 isoflavones, 3 flavanols, 3 dihydroflavonols, and 2 chalcones. Clustering analysis and PCA were used to separate the CRCP samples collected at different stages. Furthermore, from July to December, the relative contents of isoflavones, dihydroflavones, and dihydroflavonols gradually increased and flavanols gradually decreased over time. The relative content of flavonoid C-glycosides showed an increasing and then decreasing trend, reaching the highest value in August. This study contributes to a better understanding of flavonoid metabolites in CRCP at different harvesting stages and informs their potential future utilization.