As a kind of green solvent and new material, recycling of ionic liquids (ILs) especially from aqueous solution is becoming a key barrier for industrial application. In this study, concentration process of long-alkyl-chain ILs solution with nanofiltration was proposed. The influence of ion cluster on filtration performance such as volume flux (J(v)), observed rejection (R-obs) was systematically studied. Formation and properties of ion cluster including aggregation and heterogeneity were detected and validated by experiment and molecular simulation, and influence of ion cluster on membrane fouling and reuse was studied by various characterizations. Besides, the separation process was developed for typical long-alkyl-chain IL aqueous solutions with different concentrations (l-decyl-3-methylimidazolium chloride, [C(10)mim]Cl). These fundamental data will strongly support the industrial application for ILs concentration with nanofiltration technology.