As an emerging zero-dimensional nano crystalline porous material, porous organic cages (POCs) with soluble properties in organic solvents, are promising candidates as molecular fillers in mixed matrix membranes (MMMs). The pore structure of POCs should be adjusted to trigger efficient gas separation performance, and the interaction between filler and matrix should be optimized. In this work, ionic liquid (IL) was introduced into the molecular fillers of CC3, to construct the IL@CC3/PIM-1 membrane to effectively separate CO₂ from CH₄. The advantages of doping IL include: (1) narrowing the cavity size of POCs from 4.4 to 3.9 Å to enhance the diffusion selectivity, (2) strengthening the CO₂ solubility to heighten the gas permeability, and (3) improving the compatibility between filler and matrix to upgrade membrane stability. After the optimization of the membrane composite, the IL@CC3/PIM-1-10% membrane possesses the CO₂ permeability of 7868 Barrer and the CO₂/CH₄ selectivity of 73.4, which compared to the CC3/PIM-1-10% membrane, improved by 15.9% and 106.2%, respectively. Furthermore, the membrane has maintained a stable separation performance at varied temperatures and pressures during the long-term test. The proposed method offers an efficient way to improve the performance of POCs-based MMMs in gas separation.