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Dietary inhibitors of fats and carbohydrates degrading digestive enzymes can reduce obesity and type 2 diabetes. In this study, we investigated and compared polyphenol content, DPPH radical scavenging activity, and inhibitory activity on digestive enzymes, including α-glucosidase, α-amylase and lipase in flesh, peel, core and seed from mini apple (Malu domestica cv. ‘Alps Otome’). Polyphenol content was significantly higher in peel and seed extracts than in flesh and core extracts. As comparing with flesh, peel polyphenols exhibited stronger DPPH radical scavenging activity, and α-amylase and lipase inhibitory activity. Oligomeric polyphenols (Fra.II) were the main polyphenols in seed extracts, which exhibited significantly strong DPPH radical scavenging activity and inhibitory activity on digestive enzymes. However, monomeric polyphenols (Fra.I) were the main polyphenols in core extracts, which exhibited weak inhibitory activity on digestive enzymes than the other parts. Moreover, Fra.III of seed and peel extracts had the highest inhibitory activity on α-glucosidase, followed by Fra.II and Fra.I, respectively. It indicated that more highly polymerized polyphenols from peel and seed of mini apple showed more potent inhibitory activities on α-glucosidase. All of the observations suggested that mini apples possess useful properties. Particularly, it has potential applications for the treatment of diabetes and obesity.