(1) Background: Aqueous two-phase systems (ATPSs) have been widely used in the separation and purification of bioactive substances in recent years. (2) Methods: In this study, deep eutectic solvents (DESs)-based ATPSs were employed for the extraction and separation of Astragalus membranaceus polysaccharides (AMP). The optimal DES (choline chloride:urea = 1:1) was first screened to extract AMP, and the effect of DES concentration, solid–liquid ratio, pH, extraction temperature, and extraction time on the extraction yield of AMP were investigated. (3) Results: The maximum extraction yield was 141.11 mg/g under the optimum conditions. AMP was then preliminarily purified by ATPS, to further realize the recycling and reuse of DES. The effect of type of salts, salt concentration, and extraction temperature on extraction efficiency was investigated. The extraction efficiency was 97.85% for AMP under the optimum ATPS conditions. Finally, the obtained AMP was studied by molecular weight determination, infrared spectroscopy analysis, and monosaccharide composition analysis. (4) Conclusions: This ATPS extraction based on DESs is simple, environmentally friendly, low-cost, and has high extraction efficiency, which provides new ideas for the extraction of plant polysaccharides and other bioactive compounds.