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Based on the distance matrix and adjacent matrix of molecular structure, a novel topological index is proposed. A set of topological parameters is built to reflect the magnitude,shape and other structure information of the substance. The interdependency between new topological index and conductivity for alkylimidazolium cations was analyzed and a quantitative relationship to describe this interdependency was obtained using the linear analyzing method. The analysis results show that the proposed topological index is quite satisfied with higher precision of the prediction. From the molecular structure of ionic liquid, the value of conductivity can be predicted correctly. This method can be also used to predict other physical properties of the ionic liquid.