Glycyrrhiza uralensis is a common plant in many Asian and European countries, the most widely-used function in clinical is regulating property of other drugs, but the mechanism is not explicit. Fructus Cnidii (FC) is a traditional Chinese medicine, but it has mild toxicity. In order to reveal the outline of metabolite profiles for Glycyrrhiza uralensis to regulate FC toxicity, we carried out metabonomics study in rats model based on Ultra Performance Liquid Chromatography-Quadrupole-Time of Flight Mass Spectrometry (UPLC-Q-TOF/MS). All rats were randomly divided into 4 groups: W, G, S, SG. The rats of every group were orally administered on days 1 to 13. All rats urine samples were collected over night by metabolism cages. The exported LC/MS data were processed by mixOmics package of R. Pattern recognition including PCA, PLS and PLSDA function were used to analysis the trajectory for the outline of metabolite profiles. Ability of different functions was evaluated. The results showed PLSDA has more powerful discriminative ability of pattern recognition. And with the accumulation of time, the effects of licorice regulate the toxicity of FC become more and more obvious.