Thinned peach polyphenols (TPPs) were extracted by ultrasonic disruption and purified using macroporous resin. Optimized extraction conditions resulted in a TPPs yield of 1.59 ± 0.02 mg GAE/g FW, and optimized purification conditions resulted in a purity of 43.86% with NKA-9 resin. TPPs composition was analyzed by UPLC-ESI-QTOF-MS/MS; chlorogenic acid, catechin, and neochlorogenic acid were the most abundant compounds in thinned peaches. Purified TPPs exhibited scavenging activity on DPPH, ABTS, hydroxyl radical, and FRAP. TPPs inhibited α-amylase and α-glucosidase by competitive and noncompetitive reversible inhibition, respectively. TPPs also exhibited a higher binding capacity for bile acids than cholestyramine. In summary, TPPs from thinned peaches are potentially valuable because of their high antioxidant, hypoglycemic, and hypolipidemic capacities, and present a new incentive for the comprehensive utilization of thinned peach fruit.