Organic–inorganic hybrid nanocomposites within polymeric matrices have potential as functional materials for membrane gas separation. We present a new synthesis strategy for preparing novel hybrid host–guest nanocomposites by encapsulating a metal–organic complex of a transient metal such as cobalt (Co) in zeolite Y cavities with the ship-in-a-bottle (SIB) synthesis method. Then, the encapsulated zeolite Y nanoparticles were embedded into the Matrimid® 5218 matrix to fabricate a novel type of mixed-matrix membranes (MMMs) for gas separation. Eventually, the effects of incorporating these types of synthetic fillers on CO2/CH4 permselectivity of MMMs were comprehensively studied. Incorporating an encapsulated polyaza macrocyclic Co–ligand complex into the polymer matrix endowed the resultant MMM with brilliant CO2 separation performance, together with an unusual/extremely desirable enhancement in CO2/CH4 selectivity. Indeed, MMM with 15 wt% encapsulated filler loading at 35 C and 2 bar experienced a CO2 permeability of about 18.96 barrer and CO2/CH4 selectivity of about 111.7, which were more than two- and three-fold that of pure Matrimid performance. The proposed new method opens a new window to fabrication of purposeful MMMs for specific separation opportunities.