Many new citrus varieties are developed to improve their quality, but the chemical profiles of their peels are rarely investigated. In this study, the peel metabolite profiles of 13 citrus varieties were analyzed using ultra-performance liquid chromatography-quadruple time-of-flight mass spectrometry (UPLC-Q-TOF MS) and their correlation with antioxidant activity was evaluated. Among the citrus peel metabolites, 30 flavonoids, including polymethoxyflavone (PMF), and vitamin C were identified. These flavonoids contributed to the difference between the 13 citrus peels, and their relative contents varied with each variety. Hesperidin, sinestin, nobiletin, tetramethoxyflavone derivatives, and tangeretin were identified as the major flavonoids in citrus peel, while rhoifolin, margaritene, isomargaritene, catharitcin, and fortunellin were detected only in Changshou kumquat. The correlation data between the metabolite profile and antioxidant activity indicated that didymin and some polymethoxyflavones had a positive correlation with antioxidant activity, while the flavonoids in Changshou kumquat had a negative correlation. Based on these data, the 13 citrus varieties were clustered into three groups: Changshou kumquat (cluster Ⅰ), Setoka and Kanpei (cluster Ⅱ), and other varieties (cluster Ⅲ). These results provide information on peel metabolites and their distribution according to citrus varieties. However, further studies on the beneficial effects of each metabolite and citrus peel are necessary.