Eliminating the nonselective permeation path inside the mixed-matrix membranes (MMMs) is critical for fabrication of gas separation membranes. We demonstrate that by utilizing the phase separation of block copolymers, we are able to introduce metal-organic polyhedrons (MOPs) with precise pore sizes into a polymer matrix and form an ordered layered structure. We also prove that, by arranging MOP cages into a continuous nanosheet-like layer structure, we are able to generate repeated MOP-effective pathways and deplete the MOP-free permeation pathways, thus enhancing the gas-separation efficiency of MMMs.