Abstract: In this study, untargeted metabolomics technology based on ultra-high-performance liquid chromatography-quadrupole/time of flight mass spectrometry (UPLC-Q-TOF-MS/MS) was used to analyze and identify the overall chemical components of Juniperri Caulis et Folium. Chemical markers for the identification of different Juniperri Caulis et Folium species were screened by integrated principal component analysis and partial least squares discriminant analysis. A total of 58 chemical components were detected and 46 of them were identified, including 26 flavonoids, 8 organic acids and their derivatives, 4 phenylpropanoids, 3 terpenoids, and 5 other components. Among them, methylsyringin and ekersenin were identified for the first time. In the positive ion mode, 12 markers were screened, and in the negative ion mode, 13 markers were screened for species identification. In summary, UPLC-Q-TOF-MS/MS metabonomics technology combined with chemometrics method can effectively reveal the chemical composition differences of different Juniperri Caulis et Folium species, and provide reference for its species identification and quality control.