The chemical compounds and the antioxidant capacity in thinned young and ripe fruit of 7 Chinese peach and nectarine varieties were investigated. Neochlorogenic acid, catechin and chlorogenic acid were the dominant antioxidants in thinned young fruit, which were 6.4-20.7-fold, 3.3-14.2-fold, and 4.1-11.4-fold higher than ripe fruit, respectively. In addition, the sugar composition of the thinned young fruit was different from that of the ripe fruit. Sucrose displayed a markedly negative correlation with the antioxidant capacity, while glucose, fructose and sorbitol did not. Malic acid and quinic acid were the major organic acids in the thinned young fruit and were positively correlated with the antioxidant capacity. Aspartic acid and glutamic acid were the main amino acids in thinned and ripe fruit. Lysine, alanine, threonine, glycine, tyrosine, and serine were significantly correlated with the antioxidant capacities, and the correlations decreased in turn. While proline and histidine showed no marked correlation with the antioxidant capacity. The antioxidant capacity of the peaches and nectarines evaluated in terms of the DPPH and ABTS free radical scavenging activities and the ferric reducing antioxidant power (FRAP) were 1.3-11.2-fold higher in thinned young fruit than ripe fruit. In addition, the chemical composition, namely, the levels of polyphenols and sucrose, could distinguish the thinned young fruit from the ripe fruit for both peaches and nectarines.