Cholinium-based ionic liquids made of aminoate anions ([Ch][AA] ILs) have been proven to have low toxicity and to be readily biodegradable. This class of ILs has great potential as a novel phase-forming component for aqueous two-phase system (ATPS) used in protein separation. In this study, environmentally benign ATPSs were prepared by using a series of [Ch][AA] ILs (where [AA] = lysinate, ?-alaninate, glycinate, serinate) with a thermo-separable polypropylene glycol 400 (PPG 400). These [AA] anion components differ in both hydrophobicity and acid/base behavior, allowing a tunable response to the pH of the ATPS. By using the effective excluded volume theory, the phase-separation abilities of the different [Ch][AA]-based ATPSs were determined, and the trends showed good agreement with the [AA] anion hydration capacities. The partition behavior of a model protein, i.e., bovine serum albumin (BSA), was investigated by measuring the IL-rich (bottom) phase extraction efficiency and partition coefficient. The results showed that the partition behavior of the protein was governed by the hydrophobicity of the [AA] anion, whereby the BSA showed a greater affinity toward the IL-rich phase comprising a less hydrophobic [AA] anion. Furthermore, the effect of pH on the partition behavior of model proteins (i.e., BSA and trypsin) was investigated. When the pH of the system is greater than the isoelectric point pI of the model proteins and the [AA] anion, the model proteins are found to be mainly partitioned to the bottom phase. However, at a pH below the pI of the model proteins and the pI of the [AA] anion, the partitioning of model proteins favored the polymer-rich top phase. Overall, our findings demonstrate the flexibility possible in directing the target protein to a desired phase in ATPS through a proper selection of the IL s hydrophobicity and [AA] anion.