A liquid chromatography-mass spectrometry (LC-MS) method was developed for the metabonomics study of menthol cigarette effect on rats. Urines from three groups of rats were analyzed, including control rats, rats treated with menthol cigarette and rats treated with normal cigarette, and the data were processed by the method of principal component analysis (PCA). The PCA score plot showed that the metabolic difference between the rats treated with menthol cigarette and the control rats was smaller than that between the rats treated with normal cigarette and the control rats. Based on the PCA score plot, eight important metabolites, for example, kynurenic acid, were found and identified. Their relative concentration changes among the three groups further indicated that menthol cigarette maybe decrease the metabolic effect on rats.