The peels and arils from three pomegranate cultivars 'Sanbai' (SB), 'Taishanhong' (TSH), and 'Zimei' (ZM) were collected to study flavonoid profiles. Total flavonoid content (TFC) in peels was significantly higher than that in aril juices irrespective of the cultivars. Based on the widely targeted metabolomics studies by means of Ultra-performance liquid chromatographyelectrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS), a total of 210 flavonoid-related compounds were putatively identified. Multivariate statistical analyses suggested that differences from fruit fraction were larger than that from cultivar according to the flavonoid fingerprints. Pairwise comparison analysis identified the most 24, 41, and 49 differential flavonoids in SB vs. TSH in arils, SB vs. ZM in peels, and Aril vs. Peel in SB cultivar. There were 8, 3, and 21 flavonoids commonly shared in aril, peel, and cultivar comparison groups, respectively. Of the 20 annotated anthocyanins, Cyanidin 3-O-glucosyl-malonylglucoside, Rosinidin O-hexoside, Cyanidin O-syringic acid, and Peonidin O-malonylhexoside were first identified in the present study. There were 11, 9, 8, 8 differential anthocyanins filtered in peels and arils between TSH and ZM, between peels and arils in TSH and ZM, respectively. These differential accumulated anthocyanins may contribute to the color variations between TSH and ZM. The flavonoid diversity and tissue-specific distribution property in pomegranate offers a theoretical basis for further work on exploitation and utilization of flavonoids including anthocyanins in pomegranate.