In this study, we have performed molecular dynamics (MD) simulations to investigate the separation of a CO2/CH4gas mixture using 1-ethyl-3-methylimidazolium tungstophosphate ([Emim]3[PW12O40]) or ([Emim]3[Keggin]) ionic liquid confined into a carbon nanotube (CNT) at several external pressures at 300 K. We have also compared the results with the different ionic liquids (ILs), including imidazolium tetrafluoroborate ([Emim][BF4]), imidazolium hexafluorophosphate ([Emim][PF6]), and imidazolium tetrachloroaluminate ([Emim][AlCl4]). In another model, the membrane was constructed by four similar CNTs (with the confined ILs), which are almost spaced equally from each other (4ILs–4CNTs). Our results indicated the importance of polyoxometalate IL–CNT nanocomposites in the gas separation process. CNTs with [Emim]3[PW12O40] IL exhibit the highest sorption of CO2owing to the high electric charge of this particular IL. It is also totally observed that AlCl4–exhibits smaller sorption than the other ILs, especially for the 4ILs–4CNTs system for CO2sorption. The [Emim]3[PW12O40] IL in the 4ILs–4CNTs configuration exhibits more than 2 times rejection rate than the 4CNTs without IL. The diffusion coefficients of confined gas molecules in the CNT are also smallest for the [Keggin][Emim] IL, which are in agreement with the sorption and rejection results.