Our study employed Molecular dynamics (MD) simulations using BIOVIA Materials Studio 2021 software programs to analyze neat and mixed matrix membranes (MMMs) for their solubility behaviour, thermodynamics, mechanical properties, and separation properties. The d-space, followed by the Matrimid 5218 (MAT) membranes’ amorphous state, was enhanced by adding particles to their structure. Furthermore, Calix[4]arene (CA) particles lead to improved membrane physicochemical properties, such as fractional free volume (FFV), glass transition temperature (Tg), Young's Modulus (E), shear modulus (G), and bulk modulus (B), which are indicators of improved thermal resistance and transport capacity. Besides, the N₂, CH₄, and CO₂ gases’ transport properties and performance of membrane structures were analyzed in terms of their diffusivity, solubility, permeability, and selective behaviours. Based on MC simulations, increasing pressure results in a significant increase in gas adsorption, and CO₂ is more readily absorbed than N₂ or CH₄, thanks to the robust interaction between the CO₂ molecule and membrane structures. There were significant improvements in the CO₂ permeability of MMMs filled with 0.75% CA particles compared to the neat MAT. Moreover, the MMMs were found to have improved selectivity in CO₂/N₂ and CO₂/CH₄ in comparison with neat membranes. Lastly, the measuring results of transport properties indicated that the MAT-CA (0.75%) membrane is proper for industrial applications, including the treatment of natural gas.