Integrating two or more materials to construct membranes with heterogeneous pore structures is an effective strategy for enhancing separation performance. Regularly arranging these heterogeneous pores can significantly optimize the combined effect of the introduced components. Porous Organic Cages (POCs), an emerging subclass of porous materials composed of discrete molecules, assemble to form interconnected pores and exhibit permanent porosity in the solid state. A unique feature of POCs is their modularity, enabling a "mix and match" approach to create co-crystal structures driven by the intermolecular interactions. Herein, we adopted the cocrystallization strategy for fabricating gas separation membranes. We prepared membranes from a series of [4+6] imine cage pairs, which vary in cavity sizes and include cages with fluorescence properties. By optimizing the cocrystalization conditions, we successfully fabricated continuous, defect-free gas membranes, benefiting from chiral recognition interactions. By introducing regularly alternating small and large pores, we addressed challenges such as the trade-off between permeability and selectivity in gas separation membrane. Moreover, the cocrystallization strategy has been proven effective for other molecular systems besides POCs, such as macrocycles, for the preparation of co-crystal membranes. This method broadens the scope for fabricating high-performance gas separation membranes with ordered heterogeneous pores.