The solubility, diffusivity, and permeability of CO2 in three ionic liquids with a common cation were investigated by molecular dynamics simulations in order to understand the role of the anion in dictating permeability. The three ionic liquids are 1-ethyl-3-methyl imidazolium tetracyanoborate ([emim][B(CN)(4)]), 1-ethyl-3-methyl imidazolium bis-(trifluoromethylsulfonyl)imide ([emim][Tf2N]), and 1-ethyl-3-methyl imidazolium tetrafluoroborate ([emim][BF4]). The simulated solubility agrees satisfactorily with experiment with a trend of [emim][B(CN)(4)] > [emim][Tf2N] > [emim][BF4]. The higher solubility of CO2 in [emim][B(CN)(4)] appears to be due to weaker cation anion interaction, higher fraction of larger cavity, larger free volume, and more favorable interaction with CO2. CO2 diffusivity in ILs follows the same trend as solubility. On the basis of the solvation-diffusion mechanism, gas permeability was estimated and compared with experiment. The present work confirms the superiority of tetracyanoborate-based ILs for membrane-based gas separations.