In this study, a rapid, efficient, and precise UHPLC-Q-TOF-MS/MS approach was developed for the separation and identification of the main compositions in the roots of S. cathayensis for the first time. By the virtue of high resolution and high separation speed of UHPLC, and accurate MS data of Q-TOF-MS, a total of 85 components, including 35 alkaloids, 12 flavonoids, 7 terpenoids, 5 phenylpropanoids, 9 fatty acids, 7 cyclic peptides, and 10 others were identified by comparisons of their retention times, accurate masses, fragment ions, related literatures. Moreover, alkaloid, flavonoid, phenylpropanoid, and cyclic peptide were reported from S. cathayensis for the first time. This rapid and sensitive method was highly useful to comprehend the chemical compositions and will provide a scientific basis for further study on the material basis, mechanism and clinical application of S. cathayensis roots.