Chinese quince fruit is rich in proanthocyanidins (PAs), which have antioxidant properties. This work describes a method to isolate PAs from Chinese quince fruits by a combination of ball-milling pretreatment and enzyme-assisted extraction. Untreated PA fractions (UMP), ball mill pretreated PA fractions (BMP) and enzymatically hydrolysed PA fractions (BEP-1, BEP-2, BEP-3, BEP-4) were obtained. The total PA and total phenolic contents, antioxidant activity and α-amylase inhibitory activity of the six PA samples were determined, and their structural characteristics were also analyzed. BEP and BMP fractions were structurally similar with UMP, but had more total phenolics and PAs, and had higher antioxidant activities, lower thermal stability, and lower average molecular weight. Among them, BEP-4 was the most outstanding. Its total phenolics and PAs were 750.98 ± 6.95 and 948.72 ± 3.50 mg/g extract per gram dry weight, respectively. Its DPPH, ABTS, hydroxyl radical scavenging ability, and α-amylase inhibitory capacity had maximum values of 90.38%, 98.99%, 97.89%, and 92.98%, respectively. These investigations provide a new, efficient way to isolate proanthocyanidins from Chinese quince fruits, and reveal that Chinese quince fruits may be a good source of antioxidants, worthy of further development.