A new topological index (TI) was proposed based on atom characters (e.g., atom radius, atom electronegativity, etc.) and atom positions in the hydrogen-suppressed molecule structure in our previous work. In this work, the TI was used for predicting the toxicity of ILs in acetylcholin esterase (log EC50 AChE) by the multiple linear regression (MLR) method. For ILs composed entirely of cations and anions, the TIs are calculated from cations and anions, respectively. The 221 ILs used in the MLR model are based on imidazolium (Im), pyridinium (Pyi), pyrrolidinium (Pyo), ammonium (Am), phosphonium (Ph), quinolinium (Qu), piperidinium (Pi), and morpholinium (Mo). The regression coefficient (R-2) and the overall average absolute error (AAE) are 0.877 and 0.153, respectively.