Self-assembly of ionic liquids (ILs) in solution has attracted wide attention due to their potential applications in chemical and biological investigations. In this study, the aggregation behavior of 1-alkyl-3-methylimidazolium alkyl sulfate in aqueous solution was investigated by molecular dynamics simulations. The simulations reveal that interactions between tail groups play a dominant role in stabilizing the vesicle. The permeability of the vesicle was further studied, and the exchange rate of water molecules is determined by the thickness of membrane. Besides thickness, arrangement of alkyl chain of ILs in the vesicle structure influences the permeability. The interdigitated structure of tail groups in the [C(8)mim][C12SO4] system decreases the water exchange rate compared with the similar system of [C(12)mim][C8SO4]. Furthermore, the hydrogen bonding interaction and orientation analysis indicate that the orientation of the imidazolium ring provides the empty positions for water-anion interactions and promotes the water molecules to approach the hydrophobic region. These results suggest that vesicle with excellent permeability properties could be obtained by screening the hydrophilic and hydrophobic of ILs and they might be beneficial for the application in separation and drug delivery process.