At present, the structure-activity relationship of polysaccharides is a common and important focus in the fields of glycobiology and carbohydrate chemistry. To better understand the effect of specific polysaccharide structures on bioactive orientation, four homogeneous polysaccharides from Lycii fructus, one neutral along with three acidic polysaccharides, were purified, structurally characterized and comparatively evaluated on the antioxidative and anti-aging activities. The GC–MS-based monosaccharide composition analysis and methylation results showed that the LFPs had similar glycosyl types but varied proportions. Nuclear magnetic resonance (NMR) spectroscopy showed that LFPs consisted of arabinogalactan, rhamnogalacturonan and homogalacturonan structural domains. The results of the structure-activity relationship indicated that the antioxidative activity was positively correlated with the galacturonic acid (GalA) content, while the neutral multi-branched chains might be responsible for the anti-aging activity. This study is the first time to compare the principal structures and multiple biological activities of LFPs, which provided a reference for the industrial development and deep excavation of the health value of LFPs.