Chinese cherry seed protein hydrolysate (CPH) was prepared with enzymatic hydrolysis using Alcalase and Neutrase, to obtain antioxidant peptides. The CPH was gradually fractionated by ultrafiltration through 10, 5 and 3 kDa molecular weight cut-off (MWCO) membranes, then the potential sub-fraction F-IV-E(a) was gained from the active fraction F-IV (MW < 3 kDa) using gel filtration chromatography. F-IV-E(a)-4 and F-IV-E(a)-5 with the significantly higher (P < 0.05) antioxidant activities were obtained by reversed phase high performance liquid chromatography (RP-HPLC). F-IV-E(a)-4 and F-IV-E(a)-5 were identified as Phe–Pro–Glu–Leu–Leu–Ile (731.92 Da) and Val–Phe–Ala–Ala–Leu (520.61 Da) by the protein sequencer and the quadrupole time-of-flight mass spectrometer (Q-TOF MS), respectively. The results suggested that F-IV-E(a)-4 and F-IV-E(a)-5 may serve as potential antioxidants and might be evaluated as food additives, functional food and pharmaceuticals.