Ionic liquids have received lots of attention due to their physical and chemical characteristics. They are honoured the sustainable "Green Solvent". In this paper, the QSPR/QSAR (quantitative structure-property/activity relationships) method was used to study the quantitative relationship between the toxicity and structure of 43 kinds of imidazolium ionic liquids, 10 kinds of substances were used to carry out the external test. The model contains six structural descriptors selected from heuristic method, and R2, R2(CV), F and S2 of the model were 0.921, 0.894, 70.35, 0.098 respectively. Test set was used to conduct external validation, and the R2 was 0.952. The result showed that this model had good reliability, and can be used to predict the toxicity of imidazolium ionic liquids.