This study aimed at recycling flavonoids with glycolipid lowering activity from Chenpi processing residue produced by essential oil extraction. The crude Chenpi flavonoids obtained by ethanol reflux mainly contained flavonone (hesperidin) and polymethoxyflavonoids (nobiletin, tangeretin, sinensetin, and isosinensetin), which complementally exerted strong glycolipid lowering activity as revealed by digestive enzyme inhibitory activity, molecular docking and network pharmacology. The reducing sugar and water-soluble impurities were efficiently removed by yeast fermentation and aqueous two-phase system (ATPS) extraction, respectively. The optimal combination use of yeast (2 % w/v, CN36) and ATPS formed by 22 % (w/w) (NH4)2SO4 and 25 % (w/w) ethanol improved flavonoid purity to 60.25 %, enriched flavonone and polymethoxyflavonoids by 6.69-fold, and enhanced digestive enzyme inhibitory activity, which was superior to the use of individual yeast or ATPS, unoptimized combination, macroporous resin (XAD-16), and ethyl acetate. This study was the first to develop a recyclable biophysical method for simultaneous enrichment of flavonone and polymethoxyflavonoids.