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Lithium separation is of great significance to overcome the lithium supply shortage resulting from a heightened demand in the energy sector. The low selectivity of polymer nanofiltration membranes for lithium extraction from concentrated Mg/Li mixtures caused by miniaturized pore structures and weak and unstable positive surface charges limits their practical implementation. To address the surface charge strength and stability, a novel ionic liquid monomer, N1-(6-aminohexyl)-N1,N1,N6,N6,N6-pentamethylhexane-1,6-diaminium bromide (denoted as DABIL), is first synthesized and covalently anchored on a pristine polyamide thin-film composite (TFC) membrane via a secondary amidation reaction for improved selective lithium separation from Mg/Li mixtures. DABIL modification of the polyamide network contributes to increased surface hydrophilicity, an enlarged membrane pore structure, and reinforced Donnan exclusion effects. Molecular dynamics simulation confirmed that the difference of the interaction energies between water and the multication groups dominates the surface properties. The DABIL membrane exhibits sixfold enhancement of water permeability compared to the unmodified membrane and outperforms the recently reported state-of-the-art positively charged membranes. It presents an improved Li+/Mg2+ selectivity of 26.49, suggesting the membranes’ potential for lithium recovery. Moreover, the membrane shows efficient antibacterial activity for mitigating biofilm formation. We establish that functionalization of TFC membranes with ionic liquids containing multication side chains could be a promising approach to achieve improved and sustainable permselectivity for the recovery of critical metal resources.