AbstractLiquid‐liquid extraction such as an aqueous two‐phase system (ATPS) is considered a promising method in the biotechnology field for extraction of biomolecules. The binary mixture of polyethylene glycol (PEG)/salt is the most common ATPS. The ability of eutectic mixture‐based ATPS to fractionate protein macromolecules remains not well understood. Here, the role of hydrogen bond donors (HBDs) in eutectic mixtures was investigated in relation to the phase formation ability and extraction efficiency of protein. Both potassium salt and an eutectic combination were used to prepare the ATPSs. Choline chloride/urea aqueous two‐phase separation proved to be the most effective method for protein extraction. The creation of a two‐phase system and the efficiency with which a protein can be extracted from a crude solution are both affected by the choice of HBD.