A molecular dynamics simulation model was developed to comprehensively understand carbon dioxide over nitrogen (CO2/N2) selectivity through polyphosphazene-based membrane comprising of poly[bis((methoxyethoxy)ethoxy)phosphazene] (MEEP) selective layer at the molecular level. The effects of temperature, pressure, and initial feed gas composition on the CO2 transport on a polymer membrane were studied. The computed free energy and density profile of the permeating gas mixture exhibited that CO2 molecules express higher interactions with the membrane than N2 molecules, resulting in higher CO2/N2 selectivity. Statistical analysis of gas molecules (CO2, water (H2O), and N2) transportation suggested that hydro- and CO2-philic functional groups in the membrane significantly impact CO2 permeability and CO2/N2 selectivity. This study suggested that Lewis acid–base and hydrogen bonding combinations contribute to CO2 permeation and CO2/N2 selectivity. An equal CO2/N2 selectivity was observed with and without water vapor in the feed gas suggesting that water does not hinder CO2 transport through the membrane.