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The study investigated the effect of dual‐frequency ultrasound‐assisted alcohol/salt aqueous two‐phase extraction and desalination on the yield, microstructure and antioxidant properties of Astragalus polysaccharides (APS). Extracts were desalinated for 10 (APS10), 20 (APS20), and 30 (APS30) minutes. A 28.40% experimental yield, well correlated to the response surface methodology predicted model was achieved. Thermodynamic parameters were non‐spontaneous, irreversible and endothermic. Moreover, ultrasound enhanced the desalination rate and did not alter the chemical structure in the APS. Fourier Transform Infrared Spectroscopy showed a similar spectrum in all the APS samples. High‐performance gel chromatography and scanning electron microscopy, respectively presented reduced molecular weights and altered microstructures in the samples. Monosaccharide analysis revealed the existence of xylose, mannose, galactose, glucose, arabinose, rhamnose, and ribose in the APS samples. Moreover, the APS20 showed strong hydroxyl and 2,2‐diphenyl‐1‐picrylhydrazyl radical scavenging activities, thus showing its potency in reducing oxidative stress. Hence, this study demonstrates that coupled ultrasound and alcohol/salt ATPS is a sustainable technique, which generates high yields of simultaneously extracted products. Practical applications Astragalus root has been used as an effective complementary treatment to conventional medicine owing to its rich nutraceutical composition and its numerous health attributes. Commercialization of Astragalus supplements into functional foods and nutraceuticals requires continuous exploration of novel, low cost and reproducible methods that retain their bioactivity. In this work, a synergized and bio‐compatible dual‐frequency ultrasound‐assisted alcohol/salt aqueous two‐phase system was used to extract and purify Astragalus polysaccharides. Application of this technique in the nutraceutical industry reduces treatment time, lowers bulk energy consumption hence reducing energy costs. It promotes the use of low‐cost, non‐hazardous bio‐based solvents in treatment processes thus considerably reducing extraction costs and environmental degradation. Findings from this study exhibit the practicability of this technique in industrial application. It equips biotechnologists with information on improved, sustainable and safer ways of extracting and enriching the quality of nutraceutical compounds.