Mugua, fruit of the genus Chaenomeles, is a valuable source of health food and Chinese medicine. To elucidate the bioactive compounds of five wild Chaenomeles species, extracts from fresh fruits were investigated by HPLC-DAD/ESI-MS/MS. Among the 24 polyphenol compounds obtained, 20 were flavan-3-ols (including catechin, epicatechin and procyanidin oligomers). The mean polymerisation degree (mDP) of procyanidins was examined by two acid-catalysed cleavage reactions; the mDP value was the highest in Chaenomeles sinensis and the lowest in Chaenomeles japonica. Total polyphenol content (TPC) reached 46.92 and 46.28 mg/g gallic acid equivalents (GAE) in Chaenomeles speciosa and Chaenomeles thibetica, respectively, although their main bioactive compounds were different (being epicatechin and procyanidin B2 in the former, and catechin and procyanidin B1 in the latter). These two species also exhibited equally strong free radical scavenging activities. Our results further showed that the antioxidant ability of Chaenomeles fruits was significantly correlated to their total polyphenol contents. Two triterpenes (oleanolic acid and ursolic acid) were the highest quantity in Chaenomeles cathayensis and C. thibetica, respectively.