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In order to determine the effect of quaternary ammonium groups and carboxymethyl groups of chitosan on antioxidant activity, nine quaternized carboxymethyl chitosan oligosaccharides (QCMCOs) were prepared from chitosan with chloroacetic acid and 2,3-epoxypropyltrimethyl ammoniumchloride as the modifying agent under microwave irradiation. The structures of QCMCOs were characterized by FT-IR, NMR, XRD and their Mw were detected by gel permeation chromatography (GPC). The thermal stability was evaluated by thermal gravimetric analysis (TGA), and their antioxidant activities were investigated including scavenging activity of superoxide and hydroxyl radical, reducing power and metal chelating ability. The results revealed that the introduction of quaternary ammonium groups and carboxymethyl groups decreased the crystallinity and the thermal stability of chitosan oligosaccharide (COS), and their antioxidant activities were closely related to the degree of substitution of quaternary ammonium groups and the carboxymethyl groups. This study provides important guidelines for developing new antioxidant agents.