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This study revealed the effects of incorporating ionic liquid (IL) molecules: 1-ethyl, 1-butyl, and 1-octyl-3-methyl-imidazolium chlorides with different alkyl chain lengths, in interfacial polymerization (IP) on the structure and property (i.e., permeate-flux and salt rejection ratio) relationships of resulting RO membranes. The IL additive was added in the aqueous meta-phenylene diamine (MPD; 0.1% w/v) phase, which was subsequently reacted with trimesoyl chloride (TMC; 0.004% w/v) in the hexane phase to produce polyamide (PA) barrier layer. The structure of resulting free-standing PA thin films was characterized by grazing incidence wide-angle X-rays scattering (GIWAXS), which results were correlated with the performance of thin-film composite RO membranes having PA barrier layers prepared under the same IP conditions. Additionally, the membrane surface properties were characterized by zeta potential and water contact angle measurements. It was found that the membrane prepared by the longer chain IL molecule generally showed lower salt rejection ratio and higher permeation flux, possibly due to the inclusion of IL molecules in the PA scaffold. This hypothesis was supported by the GIWAXS results, where a self-assembled surfactant-like structure formed by IL with the longest aliphatic chain length was detected.