The CO2 adsorption performance of a zeolite is related to the framework structure and extra-framework composition. In this work, parent Na-GIS and partially exchanged NaMg1-GIS and NaMg3-GIS, with 30 and 50% degree of Mg2+ exchange, respectively, were prepared. Further, the series of zeolites were thoroughly characterized and studied for their applicability for CO2 adsorption and CO2/N2 and CO2/CH4 separations by single-component adsorption and dynamic breakthrough curve analysis methods. The lower concentration of Mg2+ cations in NaMg1-GIS resulted in enhanced CO2 adsorption due to beneficial distortion of the framework pore structure, making the adsorption of N2 and CH4 more challenging. However, this benefit was lost for higher Mg2+ concentration (NaMg3-GIS) due to a more pronounced framework distortion, impairing not only the adsorption of N2 and CH4 but also the CO2 one, ultimately leading to a loss of selectivity. The molecular dynamics simulations and density functional theory (DFT) calculations, aligned with experimental data, reveal an elevated heat of adsorption for CO2 in NaMg3-GIS due to framework deformation caused by Mg2+ cations. Consistent with the adsorption equilibrium experiments, the ternary dynamic experiments of CO2/N2/He evaluated by breakthrough curve analysis show a higher CO2/N2 selectivity of 1673 and 1248 at 25 and 50 °C, respectively, for the NaMg1-GIS sample. For the CO2/CH4/He experiments, the CO2/CH4 selectivity tended toward extremely high values due to negligible CH4 uptake on NaMg1-GIS. In addition, the better dynamic adsorption/separation of CO2 on NaMg1-GIS is ascribed to the greater distortion of the pore aperture due to the presence of Mg2+ cations, affecting the diffusion of small molecules. Overall, our results demonstrate the high potential of NaMg-GIS materials for critically important energy separation processes involving CO2, N2, and CH4.