The purpose of this research is to characterize and explore the feasibility of deep eutectic solvent‐based aqueous two‐phase system (DES‐ATPS) for its potential application in the extraction and purification of anthocyanins. Various combinations and molar ratios of DES using choline chloride as hydrogen bond acceptor (HBA) and butanediol (BDO), ethylene glycol (EG), and lactic acid (LA) as hydrogen bond donor (HBD) were synthesized, screened, and investigated on its physicochemical properties. The binodal phase diagrams were developed as basis for the ATPS development. It was noted that LA‐based natural deep eutectic solvents (NADES) were highly polar and likely to enhance the solubility of anthocyanin in DES. Regardless, the simple molecular structure and low viscosity of EG‐ and BDO‐based DES enhanced the solubility of anthocyanin and recorded a monomeric anthocyanin content ranging from 10.52 ± 0.78 mg cyanidin‐3‐glucoside/g at 40°C and 10.78 ± 0.84 mg cyanidin‐3‐glucoside/g at 30°C, respectively. Lastly, the liquid–liquid equilibrium binodal curves were developed and ChCl:1,3‐BDO (1:4) and ChCl:1,4‐BDO (1:4) exhibited excellent phase‐forming ability, thus concluding its excellent potential for anthocyanin extraction through ATPS.