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Lignanoids are an active ingredient exerting powerful antioxidant and anti-inflammatory effects in the treatment of many diseases. In order to improve the efficiency of the resource utilization of traditional Chinese medicine waste, Magnolia officinalis Rehder & E.H.Wilson residue (MOR) waste biomass was used as raw material in this study, and a series of deep eutectic solvents (ChUre, ChAce, ChPro, ChCit, ChOxa, ChMal, ChLac, ChLev, ChGly and ChEG) were selected to evaluate the extraction efficiency of lignanoids from MORs. The results showed that the best conditions for lignanoid extraction were a liquid–solid ratio of 40.50 mL/g, an HBD-HBA ratio of 2.06, a water percentage of 29.3%, an extract temperature of 337.65 K, and a time of 107 min. Under these conditions, the maximum lignanoid amount was 39.18 mg/g. In addition, the kinetics of the extraction process were investigated by mathematic modeling. In our antioxidant activity study, high antioxidant activity of the lignanoid extract was shown in scavenging four different types of free radicals (DPPH, ·OH, ABTS, and superoxide anions). At a concentration of 3 mg/mL, the total antioxidant capacity of the lignanoid extract was 1.795 U/mL, which was equal to 0.12 mg/mL of Vc solution. Furthermore, the antibacterial activity study found that the lignanoid extract exhibited good antibacterial effects against six tested pathogens. Among them, Staphylococcus aureus exerted the strongest antibacterial activity. Eventually, the correlation of the lignanoid extract with the biological activity and physicochemical properties of DESs is described using a heatmap, along with the evaluation of the in vitro hypoglycemic, in vitro hypolipidemic, immunomodulatory, and anti-inflammatory activity of the lignanoid extract. These findings can provide a theoretical foundation for the extraction of high-value components from waste biomass by deep eutectic solvents, as well as highlighting its specific significance in natural product development and utilization. [ABSTRACT FROM AUTHOR]