Deep eutectic solvents (DESs), a new class of green and sustainable solvents, have shown a promising application prospect in the aqueous two-phase system (ATPS) extraction. In the present work, hexafluoroisopropanol (HFIP) was introduced as a hydrogen-bond donor to synthesize DESs with choline chloride (ChCl), decyltrimethylammonium bromide, dodecyltrimethylammonium bromide, and tetradecyltrimethylammonium bromide (hydrogen-bond acceptor), respectively. These HFIP-based DESs (HFIP-DESs) can form ATPS with various inorganic salts, and their phase separation ability is significantly stronger than that of small molecule aliphatic alcohols, HFIP, and traditional DESs. The ATPSs based on HFIP-DESs were first used to extract anthraquinones (AQs) from Rhei Radix et Rhizoma samples. Under the optimal conditions, more than 92% of AQs (including aloe-emodin, rhein, emodin, chrysophanol, and physcion) was enriched in the DES-rich phase of the ATPS composed of ClCl-HFIP DES and Na2SO4. Compared with the traditional chloroform extraction method (60 mL chloroform consumption), the ChCl-HFIP DES/Na2SO4 ATPS extraction method attained high extraction efficiency but only consumed 0.5 mL of organic solvent (HFIP).