The various apple products industries produce a large amount of apple residue, which is easily fermented, causes environmental pollution, and its disposal cost is high, but is rich in nutrients, such as polyphenols. Polyphenols can be purified to realize high-value deep processing of apple pomace and to promote energy reuse of food waste. In this study, the highly selective purification of polyphenols was achieved by membrane filtration using prepared Metal-organic framework (MOF)-5/PES mixed matrix membranes with apple peels as raw material. The polyethersulfone mixed matrix membrane was loaded with MOF-5 by the phase inversion method, and their structural and physicochemical properties were characterized by scanning electron microscopy (SEM), and X-ray diffraction (XRD). Zeta potential and specific surface area of MOF-5 particles were measured, as well as the water contact angle and anti-fouling properties of the mixed matrix membrane were analyzed. It was confirmed that the membrane loaded with MOF-5 showed better hydrophilicity and mechanical properties compared with the pristine polyether sulfone membrane. Under practical conditions, the increased hydrophilicity could enhance the anti-fouling properties of membranes, which would improve the flux recovery ratio of membranes. In addition, the prepared MOF-5/PES mixed matrix membrane was applied to the purification of polyphenols, showing excellent purification performance of polyphenols. In particular, the purity of polyphenol after membrane filtration could reach 70.45% when the additional amount of MOF-5 was 10%. This research provides a method to prepare MOF-5/PES mixed matrix membranes, which effectively solves the problem of unstable and unsatisfactory purification effect of commercially available membranes, promotes the development of new materials in membrane science, and realizes high-value deep processing and comprehensive resource development of food waste using membrane filtration.