PEG-based aqueous two-phase systems (ATPS) for extraction and removal of metal ions from industrial wastewaters is a promising strategy to replace traditional organic-aqueous two phase systems, due to its environmentally friendly advantages and excellent separation efficiency from controllable phase structure and physicochemical properties. However, controversy still remains about the partitioning mechanism of metal ions into the PEG-rich phase in ATPS. The present contribution revealed that a specific hydrophobic interaction was a main driving force for the transferring of Cr(VI) ions into the PEG-rich phase in ATPS. The properties of aqueous media around the PEG molecules and Cr(VI) ions also played a crucial role in the partitioning of Cr(VI) ions in the PEG-base ATPS. The PEG-rich phase in the ATPS exhibited a specific affinity toward poorly hydrated HCrO4- ions, compared to the strongly hydrated CrO42- ions. The difference in the properties of aqueous media in the coexisting liquid phases was response for the partitioning of Cr(VI) ions in the PEG-base ATPS. It was confirmed by combined application of UV vis spectroscopy and molecular dynamics simulations. The present work provides a new understanding into the microscopic mechanism of the partitioning of metal ions in the polymer-based ATPS.