In this work, three kinds of ether-functionalized pyridinium-based ILs [EnPy][NTf2] with low viscosity were designed and synthesized and used for highly selective separation of CO2 from CH4. It was found that the ether groups play an important role on physicochemical properties and CO2/CH4 selectivity in these three ILs. Compared with the nonfunctionalized analogues [CmPy][NTf2], the viscosities of [E(n)PA [NTf2] are lower and obviously decrease with the increasing number of ether oxygen atoms. The presence of ether groups on the cation has weak impacts on CO2 solubility of the ILs, but it contributes to a much lower CH4 solubility, which leads to the great increase of CO2/CH4 selectivity using [E(n)PA][NTf2]. Moreover, CO2/CH4 selectivity in all investigated ILs greatly decreases with the increasing temperature due to the weaker temperature dependence of CH4 solubility. In addition, the thermodynamic properties including the Gibbs free energy, enthalpy, and entropy of CO2 and CH4 in these ILs were also obtained, and the CO2 and CH4 dissolution mechanisms were further analyzed. The results demonstrated that the gas-IL interaction plays a dominate role in CH4 solubility in the investigated ILs, but CO2 dissolution in ILs is determined by both the IL-gas interaction and free volume of ILs. This work will offer new insights into designing more competitive ILs for selective separation of CO2 from CH4.