This study employs molecular dynamics (MD) simulations to fundamentally provide insight into the role of cross-link density in the CO2 separation properties of interfacially polymerized polyamide (PA) membranes. For this purpose, two atomistic models of pure polyamide membranes with different cross-link densities are constructed by MD simulations to conceptually determine how the fractional free volume of polyamide affects the gas separation performance of the membrane. The PA membrane with a lower cross-link density (LCPA) shows a higher gas diffusion coefficient, a lower gas solubility coefficient, and a higher gas permeability than the PA membrane with a higher cross-link density (HCPA). Moreover, the pristine and modified silicate nanotubes (SNTs) as the fast gas transport channels are incorporated into the polyamide membranes to assess the effect of the SNT/PA interface chemistry on the CO2 separation properties of the membranes. SNTs are systematically modified by three modifying agents with different CO2-philic groups and different interfacial interaction energies with the polyamide matrix. The results of MD simulations demonstrate that the incorporation of silicate nanotubes into the PA matrix increases the gas diffusivity and permeability and decreases the CO2/gas selectivity. Moreover, the membranes containing modified SNTs possessing high CO2-philicity and high SNTs/PA interfacial interactions show a high CO2 separation performance.