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Nowadays, natural gas is one of the most important clean energy sources. In order to meet the demand for natural gas purification, a comprehensive experimental scheme is designed in this paper, which involves porous material construction, host-guest assembly, membrane preparation, structural characterization, and performance analysis, achieving innovative research on new mixed matrix membranes. Herein, a porous organic cage is explored as the filler, and its pore size is further regulated through the assembly of ionic liquids inside its pores. Gas separation results show that the mixed matrix membrane with ionic liquid assembly exhibits excellent CO2/CH4 separation performance, which increases by 50.4% and 245.3% respectively compared to the polymer membrane and the mixed matrix membrane without ionic liquid assembly, and remarkable pressure and long-time stability, which provides a new idea for the application of porous organic cages in the area of separation membrane, and also provides a new idea for the design of natural gas purification membrane materials.