Aucubin (AU) is an active ingredient that exerts strong antioxidant and anti-inflammatory effects in the treatment of several diseases. In order to improve the efficiency of resource utilization of traditional biomass waste, Eucommia ulmoides seeddraff (EUSD) waste biomass was used as the raw material, and a series of deep eutectic solvents were selected to evaluate the extraction efficiency of aucubin from EUSD. A response surface experiment was designed based on a single-factor experiment to optimize the extract conditions. The results showed that the best conditions for aucubin extraction were an HBD−HBA ratio of 2.18, a liquid−solid ratio of 46.92 mL/g, a water percentage of 37.95%, a temperature of 321.03 K, and an extraction time of 59.55 min. The maximum amount of aucubin was 156.4 mg/g, which was consistent with the theoretical value (156.8 mg/g). Then, the performance of 12 resins for adsorption and desorption was contrasted. The results revealed that HPD950 resin exhibited the best performance, with an adsorption capacity of 95.2% and a desorption capacity of 94.3%. Additionally, the pseudo-second-order model provided the best match to the kinetics data, the Langmuir model provided the best fit to the isotherm data, and adsorption was a beneficial, spontaneous, exothermic, and physical process. In the recyclability test, the HPD950 resin had great potential and excellent sustainability in aucubin recovery. In the antioxidant activity study, the aucubin extract exerted a strong antioxidant ability with scavenging capabilities for four free radicals. Furthermore, the antifungal activity study found that the aucubin extract exhibited a good antifungal effect against 5 tested pathogens. The research results can provide a theoretical basis for the extraction of high-value components from waste biomass by deep eutectic solvent and a certain application value for the development and utilization of natural aucubin products.