The objectives of this study were to evaluate the effect of different functional groups of sulfate, amine, and hydroxyl and/or their ionized groups on in vitro antioxidant capacities of low-molecular-weight polysaccharides (LMPS) prepared from agar (LMAG), chitosan (LMCH), and starch (LMST), respectively, and to elucidate their structure-activity relationship. Ascorbic acid and ethylenediaminetetraacetic acid (EDTA) were used as positive controls. The in vitro antioxidant capacities of LMAG and LMCH were higher than that of LMST in the DPPH radical, superoxide radical, hydrogen peroxide, and nitric oxide radical scavenging and ferrous metal-chelating capacities. The different scavenging capacities may be due to the combined effects of the different sizes of the electron-cloud density and the different accessibility between free radical and LMPS, which, in turn, depends upon the different hydrophobicities of the constituent sugars.