Due to the diversity and complexity, the change of chemical components in medicinal plant according to the time, cultivated varieties or ecological condition is difficult to recognize using traditional phytochemistry method. In order to analyze the pharmacodynamics material basis in Uighur medicinal plant Artemisia rupestris L. in an effective and comprehensive way, a plant metabolomics approach was established based on liquid chromatography-tandem mass spectrometry (LC-MS/MS). This study firstly focused on the effect of extraction solvents,redissolve solvents and ultrasonic time on the untargeted metabolomics, then the optimal preparation condition was selected according to metabolites coverage. After methodology validation, the approach was applied to acquire metabolic information in root, stem, branchlet, leaf and flower of Artemisia rupestris L. The results showed that the metabolome in flower was obviously different with the other organs. Coupling with multivariate statistical analysis, a batch of differential metabolites were picked out, in which 61 flavonoids, 97 rupestonic acid derivatives, 7 chlorogenic acids and 15 other compounds were primarily recognized according to the characteristic fragmentation rules of specific structure type and database retrieval. Additionally,the distribution characteristics of the above 180 differential metabolites was illustrated by cluster heat map. In conclusion,this study provided important information about the rational utilization of effective parts from Artemisia rupestris L.,and offered a novel strategy for quality control,variety improvement and reasonable development of medicinal plants.