ETS-4 shows great potential to achieve effective separation of challenging mixtures due to its promising tunability of pores. However, the regulation of pore size is largely limited by its low thermal stability. Here, Na-ETS-4 was synthesized by the hydrothermal method and additionally modified via ion exchange coupled with thermal treatment. Structures of all synthesized samples were examined using a variety of characterization techniques. Both adsorption equilibrium and kinetics of CO2and CH4on these adsorbents were evaluated on custom-made adsorption units. In addition, the mechanism of CO2adsorption on different structural models of ETS-4 was revealed via combining with the molecular dynamics (MD) simulations. Ion exchange largely improves the thermal stability of ETS-4 and its adsorption capacities for CO2and CH4. Ba-ETS-4-350 exhibits the largest equilibrium selectivity of 12.42 and the greatest Henry’s selectivity of 2178.51. The radial distribution function (RDF) results reveal the main adsorption sites of CO2in different ETS-4 structures.