Boron and copper heteroatoms were successfully incorporated into the frameworks of high-silica RHO zeolite by adopting a bulky alkali-metal-crown ether (AMCE) complex as the template. These heteroatom-doped zeolites show both larger micropore surface areas and volumes than those of their aluminosilicate analogue. Proton-type RHO zeolites were then applied for the separation of CO2 /CH4 /N2 mixtures, as these zeolites have weaker electric fields and, thus, lower heats of adsorption. The adsorption results showed that a balance between working capacity and adsorption heat could be achieved for these heteroatom-doped zeolites. Ideal adsorbed solution theory predictions indicate that these zeolites should have high selectivities even for remarkably dilute sources of CO2 . Finally, the heteroatom-substituted zeolites, especially the boron-substituted one, could be thermally regenerated rapidly at 150 °C after full hydration and maintained high regenerability for up to 30 cycles; therefore, they are potential candidates for trace CO2 removal under humid conditions.