The recovery of wastewater proteins is gaining more attention in environmental protection. In the present work, phase diagram of the [C(n)mim]X (n = 4, 6, 8; X = Cl and Br) + K2HPO4 aqueous two-phase systems have been determined, and the aqueous two-phase systems have been used to remove bovine serum albumin (BSA), lysozyme, and hemoglobin from the simulated wastewater. The influence of pH value, the composition of the aqueous two-phase systems, and the temperature of the systems on the partitioning of the proteins has been studied. It has been found that 76-100% of the proteins could be extracted into the ionic liquid-rich phase in a single step partition. The partition coefficients of lysozyme slightly increases but those of BSA and hemoglobin decrease with increasing tie line length (TLL). The higher extraction efficiency of the proteins is achieved at the pH value close to their isoelectric point and under higher temperatures. The results indicate that the IL-based aqueous two-phase systems have the potential for the separation of wastewater proteins.