The gas separation industry has witnessed a significant focus on mixed matrix membranes (MMMs) due to their exceptional potential, surpassing the performance of conventional polymeric membranes. This study aimed to develop and evaluate MMMs using polyurethane (PU) as the polymer matrix and zinc oxide (ZnO) and ionic liquids (ILs) as fillers. PU/ZnO, PU/IL, and PU/ZnO/IL MMMs were prepared utilizing the dry-phase inversion method, and their efficacy in separating CO₂, CH₄, and N₂ gases was investigated under various conditions. A comprehensive characterization protocol using FTIR, FESEM, TGA, AFM, and tensile testing was employed for their thorough characterization. The membranes’ transport properties were assessed at different pressures and filler concentrations. Results showed that IL incorporation increased gas permeability by enhancing solubility, diffusion, ionic interactions, swelling, and accessible volume. Incorporating ZnO and IL particles in the PU matrix simultaneously improved transport properties, particularly selectivity. Robeson's diagram analysis shows that the PU/0.5%ZnO/2%IL MMM performed best. Furthermore, molecular simulation methods, including Monte Carlo and molecular dynamics simulations, assessed adsorption isotherms and physicochemical properties such as free volume, density, and X-ray diffraction. Simulation outcomes were highly reliable with experimental results, affirming the results’ efficiency and validation. Overall, this study demonstrated the efficiency of using ZnO and IL in the MMMs, highlighting their potential in gas separation applications.