Many of the mixed matrix membranes (MMMs) face the challenge of fillers agglomeration. In this paper, the gas separation performance of MMMs based on poly (ether-block-amide) (PEBA, 60 wt% PEO and 40 wt% PA6) filled with different functionalized zeolite faujasite (FAU, X-type) fillers was investigated. To improve the interfacial adherence of the fillers with PEBA chains, Nafion (R) and 3-aminopropyl triethoxysilane (APTEOS) were used as sulfonic acid and aminosilane functionalizing agents, respectively. Different physicochemical and morphological characterizations such as XRD, FTIR, SEM, AFM, thermal, and mechanical tests were used to characterize the prepared membranes. The prepared membranes were evaluated for single gas and mixed gas separation performances. The results showed that CO2 permeability reached to 110 and 122 Barrer for sulfonic acid- and amine-FAU (1 wt%) filled PEBA, respectively. In addition, amine-MMM (1 wt%) had better performance for CO2/N-2 selectivity (117), while SO3-MMM (1 wt%) showed higher CO2/CH4 selectivity (31) due to their intrinsic properties. Molecular simulation was also carried out to study the structural and transport properties of the fabricated membranes. The solubility and diffusivity of CO2, CH4, and N-2 gas molecules were studied by Grand Canonical Monte Carlo (GCMC) and Molecular Dynamics (MD) methods, respectively. The acquired results revealed that experimental and simulation data were consistent in approach.