Plant polyphenols are potential substitutes for clinical α-glucosidase inhibitors. Our previous studies indicated that prodelphinidins from Chinese bayberry leaves (BLPs) have stronger α-glucosidase inhibitory activity than other common polyphenols, but they have no safe history of consumption. There is a reasonable prospect that prodelphinidins from Chinese bayberry fruits (BFPs) can improve postprandial hyperglycemia, though known active components are only myricetin and cyanidin-3-O-glucoside. Hence, the aim of this study was to analyze structure and hypoglycemic effect of BFPs of “Biqi” (BQPs) and “Dongkui” (DKPs) cultivars, and compare their difference with BLPs. The contents of BQPs and DKPs were (221.73 ± 0.60) and (136.82 ± 4.33) mg epicatechin (EC) equivalents/g dry weight, respectively. The most subunits were epigallocatechin gallate along with a small amount of epigallocatechin, epicatechin gallate and EC connected by B-type linkages and a small portion of A-type linkages with mean polymerization degree of 4.25 and 4.08, respectively. Importantly, BQPs and DKPs were α-glucosidase inhibitors with half inhibitory concentration of 11.91 and 9.47 μg/mL respectively, which were significantly stronger than BLPs. DKPs could also improve postprandial hyperglycemia of normal mice and high fat diet-induced type II diabetic mice. Therefore, edible prodelphinidins, which have stronger hypoglycemic effect than BLPs, were first found in Chinese bayberry fruits.