Abstract: Heracleum moellendorffii contains abundant bioactive components such as flavonoids and polysaccharides. However, their efficient extraction and utilization face challenges. This study aimed to develop an efficient ultrasound-assisted aqueous two-phase extraction technique for the simultaneous extraction of flavonoids and polysaccharides from Heracleum moellendorffii. The extracted flavonoids and polysaccharides were formulated into an oil-in-water microemulsion to enhance the in vitro hypoglycemic and hypolipidemic activities of Heracleum moellendorffii, thereby providing a novel approach for the high-value utilization of Heracleum moellendorffii. First, the phase diagram of the polyethylene glycol-ammonium sulfate aqueous two-phase system was plotted using the cloud point method to identify the suitable biphasic region. Key factors influencing extraction efficiency were screened through single-factor experiments and Plackett-Burman tests, and then the extraction process was further optimized using Box-Behnken response surface methodology. The optimal conditions as follows: Liquid-to-material ratio of 34.5:1 mL/g, ultrasonic time of 41 min, and extraction temperature of 51 ℃. Under these conditions, the extraction yields of flavonoids and polysaccharides were 0.54% and 10.03%, respectively. The extracts were purified and used to prepare the Heracleum moellendorffii flavonoid-polysaccharide oil-in-water microemulsion. The resulting microemulsion appeared as a pale yellow, clear, and transparent liquid with an average particle size of 140.80 nm, a Zeta potential of −19.36 mV, and a flavonoid encapsulation efficiency of 85.31%. In vitro activity results indicated that the Heracleum moellendorffii flavonoid-polysaccharide microemulsion showed sodium glycocholate and sodium taurocholate binding rates of 59.92% and 56.91%, respectively, along with a pancreatic lipase inhibition rate of 78.89%, demonstrating promising potential for lipid-lowering effects. Furthermore, this microemulsion exhibited good inhibitory activity against α-glucosidase and α-amylase, with IC₅₀ values of 13.61 mg/mL and 12.69 mg/mL, respectively. This study provides a theoretical foundation and technical support for the efficient utilization of active components from Heracleum moellendorffii and the development of functional foods.