Ionic liquid-based aqueous biphasic systems (IL-based ABSs) are considered as promising extraction and purification routes. For designing an efficient process of protein extraction, it is necessary to complete information about phase diagrams including binodal and tie-lines for new ABSs. In this respect, here, binodal curves and tie-lines for ternary aqueous solutions composed of polypropylene glycol 400 and some of choline amino acid ionic liquids, [Ch][AA]-ILs, including choline L-histidine, choline L-arginine, choline L-proline, and choline L-valine as a green and biocompatible entrainers have been determined at T = 298.15 under atmospheric pressure (≈85 kPa). The results indicated that the binodals of these ABSs affected strongly by the ILs structures; so that, biphasic region is increased by decreasing of hydrophobicity of IL anion from valine to arginine. The effective exclude volume theory (EEV) and Setschenow equation have been utilized for addressing phase formation capability in these systems. Phase formation ability in these ABSs followed in the order: choline L-arginine > choline L-histidine > choline L-proline > choline L-valine which is parallel with an increasing hydrophilicity of amino acid exists in each of IL structures. Moreover, osmotic virial equation was used for modeling of tie-lines in the studied ABSs. Finally, the performance of these ABSs for separation of biomolecules was evaluated by studying the partition behavior of bovine serum albumin, BSA, via measuring of partition coefficient and extraction efficiency. The obtained results from BSA partitioning in these ABSs indicated that BSA is migrated preferentially to the [Ch][AA]-ILs-rich bottom phase and this migration is increased by increasing hydrophilicity of amino acid exists in IL structure, i.e. choline L-arginine > choline L-histidine > choline L-proline > choline L-valine. Also, it was found that the salting-out effect and π-π interactions between BSA and [Ch][AA]-ILs have important role in BSA partitioning as well as hydrophilicity/hydrophobicity interactions.