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In the course of our research on utilizing edible flower resources to promote health, five ellagitannins (1–5) were isolated from pomegranate (Punica granatum L.) flower by bioassay-guided fractionation. Among them, mallotusinin (1) and tercatain (2) were first isolated from pomegranate flower, and punicatannin D (4) was an unprecedented compound. Compounds 1–3 exhibited significant xanthine oxidase (XO) inhibitory activity compared with allopurinol, and a potent inhibition on α-glucosidase that was superior to acarbose was observed for compounds 1–4. The XO inhibitory activity is positively correlated with the amount of galloyl moiety (3 > 2 > 1). Presenting tetrahydroxydibenzofuranoyl substituent or increasing the number of galloyl group enhanced the inhibition capacity of α-glucosidase (1 > 3 > 2). The inhibitory mechanism was further clarified in terms of kinetic studies and molecular docking. This study revealed that the ellagitannins present in pomegranate flower might be promising functional food ingredients with anti-hyperuricemia and anti-hyperglycemia properties.