The high polysaccharide content of Lycii fructus agri-food waste should be reclaimed for value liberation from both environmental and economic perspectives. In this study, waste from L. fructus pigment products was valorized on a bench scale by upcycling into active polysaccharide-rich extracts. The methodological feasibility of polysaccharide recovery from L. fructus waste was evaluated using sequential extraction techniques. Three fractions LFP-30, LFP-100, and LFP-121, were obtained under stepwise increases in temperature and pressure. Highly heterogeneous xyloglucan (XG)-pectin macromolecules composed of linear homogalacturonan (HG) and alternating intra-RG-I-linkers, with topological neutral branches and XG participation, were predominant among the L. fructus polysaccharides (LFPs). Antioxidant activities in LFPs were unaffected by waste resources and severe extraction methodology conditions. Additionally, the direct investment potential of polysaccharide recovery was evaluated for full-scale implementation. This study demonstrated the necessity and feasibility of extracting bioactive polysaccharides with potential applications from L. fructus waste, and provided a sustainable strategy for transforming L. fructus waste disposal problems into value-added products using cost-effective methodologies.