On the basis of the new topological index (TI) proposed in our previous work, a multiple linear regression (MLR) model was developed for predicting the toxicity of ionic liquids (Its) in Leukemia Rat Cell Line (log EC50 IPC-81). The TI is derived from atom characters (e.g., atom radius, atom electronegativity, etc.) and atom position in the hydrogen-suppressed molecule structure. Because ILs are composed entirely of cations and anions, the TIs are calculated from cation and anion, respectively. A third TI was also proposed to depict the interaction of anion and cation. The toxicity of 173 ILs, which are based on imidazolium (Im), pyridinium (Py), pyrrolidinium (Pyr), ammonium (Am), phosphonium (Ph), quinolinium (Qu), piperidinium (Pi), and morpholinium (Mo), was calculated by the model. The regression coefficient (R-2) and the overall average absolute error (AAE) are 0.938 and 0.226, respectively.