Blending an aromatic-selective ionic liquid (IL, namely 1-ethyl-3-methylimidazolium hexafluorophosphate, [emim][PF₆]) with waterborne polyurethane (WPU) enabled us to obtain [emim][PF₆]-modified waterborne polyurethane composite membranes. We characterized the structure and properties of the [emim][PF₆]/WPU composite membranes by ATR-FTIR, DSC, UV, SEM, EDX, swelling tests, and pervaporation testing. Characterization of the change in the morphology of the membranes in response to the IL loading indicated that a preferential interaction between the IL and soft segments of WPU was induced by hydrogen bonding. This interaction inhibited a potential interaction with benzene (Bz), which initially lowered the permeability. However, at high IL loading, the IL incorporation became ineffective owing to macrophase separation, which caused an increase in the permeability, as indicated by the SEM results. Swelling testing of the [emim][PF₆]/WPU composite membranes showed that the membranes exhibited preferential adsorption of Bz, and the swelling degree of the composite membranes in Bz solvent increased from 58% to 98% and remained almost constant in cyclohexane solvent as the IL content was increased. The [emim][PF₆]/WPU composite membranes enhanced the separation selectivity of Bz/Cy for an IL loading < 10 wt%. The best separation factor was 8.4, and the total flux was 0.19 kg (m² h)⁻¹ (50 wt% Bz/Cy mixtures at 50 °C) at w([emim][PF₆]) : w(WPU) = 10 : 100. In addition, the composite membrane exhibited excellent stability over long-term operation. These results demonstrated that the [emim][PF₆]/WPU composite membranes could be effective for separation of Bz/Cy mixtures by the pervaporation method.