Cytotoxicity studies are important tools for the assessment of the toxicity of ionic liquids (ILs). In the present study, the cytotoxicity of eleven ILs against Spodoptera frugiperda 9 (Sf-9) cell lines were evaluated via 344,5-dimethylthiazol-2-y1)-2,5-diphenyltetrazolium bromide (MTT) assays. The effect on cellular morphology, ultrastructural morphology, and nuclear morphology induced by 1-ethyl-3-methylimidazolium bromide ([C(2)mim] [Br]) was studied via inverted light microscopy observation, acridine orange staining, and transmission electron microscope (TEM) analysis, respectively. The effect on cell DNA fragmentation, cell apoptosis and cell cycle induced by [C(2)mim] [Br] was also investigated via DNA agarose gel electrophoresis and flow cytometry analysis, respectively. The results showed that the cytotoxic effect of ILs on Sf-9 cells was related to the IL structures, concentrations, and length of exposure. The morphological features of apoptosis induced by [C(2)mim] [Br] such as cell shrinkage and convolution, apoptotic bodies, pyknosis, and karyorrhesis were observed. All these phenomena confirmed that Sf-9 cells exposed to [C(2)mim] [Br] died via apoptosis. This study complements the current knowledge about the cytotoxic properties of ILs on insect cells and highlights the mechanism by which ILs kill these cells. Furthermore, it provides a basis for further studies on the future applications of ILs as insecticides.