“Nine-processed” tangerine peel (Jiuzhi Chenpi) is a special snack in Guangdong, China, which is made by traditional and complex techniques. However, it is not clear how the flavonoid composition changes during its complex processing. In this study, we employed UPLC-ESI-Q Trap-MS/MS to comprehensively evaluate the alterations in flavonoids metabolites at four key processing stages: raw materials (CP1), soaking (CP2), curing (CP3), and aging (CP4). The results showed that total of 165 flavonoids metabolites were detected. Naringin, narirutin, hesperidin, neohesperidin and 3,5,6,7,8,3′,4′-heptamethoxyflavone were the top five compounds in terms of the relative content (>5.00%), and their relative content did not change significantly during processing. From CP1 to CP4, the relative content of 38 compounds, including 3′,4′,5,6,7-Pentamethoxyflavanone, apigenin 6,8-C-diglucoside, and diosmin, decreased continuously during processing. The relative contents of astragalin, naringenin-7-O-glucoside and apigenin-7-O-β-D-glucoside were increased by 2.06 times, 2.12 times and 3.34 times, respectively. Isorhamnetin-O-hexoside-O-pentoside (1.98%), 2,4,4′-trihydroxychalcone (0.43%), daidzein-hexoside-xyloside (0.03%), acacetin-7-O-galactoside (0.03%), chrysin-O-glucoside (0.01%), glycitein (0.01%), and prunetin (0.01%) were only detected in CP4. Correlation analysis showed that total flavonoids and naringin were significantly positively correlated with antioxidant activity. These findings offer valuable insights into the metabolites of “nine-processed” tangerine peel during processing and provide a basis for process optimization and quality control.