The development of advanced functional materials is a growing field to improve the performance of mixed matrix membranes (MMMs) as energy efficient alternatives to the conventional gas separation membranes. Herein, a novel highly selective host–guest complex was synthesized by encapsulating a Schiff base macrocyclic copper complex in the FAU super-cages of zeolite 13X. The design strategy of the encapsulated complex is based on the utilization of the same polymer's monomer, durene diamine monomers, as the Schiff base ligand component to eliminate interfacial defects, and also improve the CO2-facilitated transport through the favorable functional groups. MMMs comprised of ([Cu(6L)]2+@13X) and the as-synthesized 6FDA-durene polyimide were investigated. The MMM containing 15 wt% of the [Cu(6L)]2+@13X complex resulted in the CO2 permeability of 1034.1 barrer with CO2/CH4 and CO2/N2 selectivities of 42.2 and 38.3, respectively. These results are 127%, 173% and 173% higher than that of the pristine 6FDA-durene, which showed the CO2 permeability of 455.2 barrer with CO2/CH4 and CO2/N2 selectivity of 15.4 and 14.0, respectively. Thus, the superior results of the present work suggest that encapsulated Schiff base transition metal complexes containing polymeric matrix monomers offer a new route to produce advanced functional fillers for highly effective gas separation MMMs.