Among various applications, ionic liquids (ILs) have been used as antimicrobial agents in laboratories, possibly through induction of the leakage of bacteria. A molecular-level understanding of the mechanism that describes how ILs enhance the permeation of membranes is still lacking. In this study, the effects of imidazolium-based ILs with different alky chain lengths on the structure and phase behavior of 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE), which is a representative bacteria-membrane-rich lipid, have been investigated. By employing differential scanning calorimetry and synchrotron small- and wide-angle X-ray scattering techniques, we found that ILs with longer alkyl chains influenced the phase behavior more effectively, and lower IL concentrations are needed to induce phase separation for both lamellar liquid crystalline phase and nonlamellar inverted hexagonal phase of POPE. Interestingly, the IL with an alkyl chain of 12 carbon atoms ([C-12 mim]Cl) shows a difference. It exhibits a stronger disturbing effect on the POPE bilayer structure than [C-16 mim]Cl, indicating that the ability of ILs to influence the membrane structures is dependent not only on the alkyl chain length of ILs, but also on the degree of matching of the alkyl chain lengths of ILs and lipids. The new lamellar and nonlamellar structures induced by ILs both have smaller repeat distances than that of pure POPE, implying thinner membrane structures. Data of the fluorescence-based vesicle dye leakage assay are consistent with these results, particularly the defects caused by IL-induced phase separation can enhance the membrane permeability markedly. The present work may shed light on our understanding of the antimicrobial mechanism of ILs.