Ionic liquids (ILs) have been widely considered and used as "green solvents" for more than two decades. However, their ecotoxicity results have contradicted this view, as ILs, particularly hydrophobic ones, are reported to exhibit high toxicity. Yet the origin of their toxicology remains unclear. In this work, we have investigated the interaction of amphiphilic ILs with a lipid bilayer as a model cell membrane to understand their cytotoxicity at a molecular level. By employing fluorescence imaging and light and X-ray scattering techniques, we have found that amphiphilic ILs could disrupt the lipid bilayer by IL insertion, end-capping the hydrophobic edge of the lipid bilayer, and eventually disintegrating the lipid bilayer at high IL concentration. The insertion of ILs to cause the swelling of the lipid bilayer shows strong dependence on the hydrophobicity of IL cationic alley chain and anions and is strongly correlated with the reported IL cytotoxicity.