Mixed matrix membranes (MMM) based on 6FDA-Durene polyimide are one of the most widely studied polymeric materials for CO₂/N₂ and CO₂/CH₄ separation. The performance of existing 6FDA-Durene membranes is a bottleneck for widespread deployment in industrial applications due to the trade-off between permeability and selectivity. It is hypothesized that membrane performance is enhanced by functionalization of the filler. However, the preparation and experimental study of defect-free functionalized MMMs that exhibit improved CO₂/N₂ and CO₂/CH₄ separation performance is challenging at the laboratory scale and requires prior knowledge of the compatibility between the filler and the polymer. Molecular simulation approaches can be used to investigate the effect of functionalization on the gas transport properties of MMMs at the atomic level without the challenges inherent in experimental study. However, they have been less investigated to date. Furthermore, most of the research has focused on pure gas studies, while mixed gas transport properties that demonstrate true separation in functionalized zeolite 13X/6FDA-Durene mixed network membranes are rarely available. In this work, a molecular simulation computational framework was developed to investigate the structural, physical properties and gas transport behavior of amine-functionalized zeolite 13X/6FDA-Durene-based MMM. The effect of different filler loadings (i.e., 5 to 15 wt%) on the physical properties and gas transport properties of amine-functionalized Zeolite 13X/6FDA-Durene MMM was also investigated at 298 K and 2 bar pressure. Functionalization of zeolite 13X nanoparticles increases the diffusion and solubility coefficients, leading to increased permeability (94%) and selectivity towards N2 and CH4 for amine-functionalized zeolite 13X/6FDA-Durene MMMs by 78% and 40%, respectively, compared to zeolite 13X/6FDA-Durene based MMMs at an optimal loading of 15%. The findings of this study can help improve the real separation in the design and concept of future functionalized MMMs using molecular simulation and experimental modeling methods.