Patrinia scabra Bunge has long been used in clinic as a traditional Chinese medicine for treating leukemia and cancer and regulating host immune response. Despite their wide use in China, no report on system analysis on their chemical constituents is available so far. The current study was designed to profile the fingerprint of ethyl acetate extract of it, and in addition, to characterize the major fingerprint peaks and determine their quantity. Therefore, a detailed gradient high-performance liquid chromatography was described to separate more than 30 compounds with satisfactory resolution in P. scabra Bunge. Based on the chromatograms of 10 batches samples, a typical high-performance liquid chromatographic (HPLC) fingerprint was established with 23 chromatographic peaks being assigned as common fingerprint peaks. Furthermore, a quadrupole time of flight mass spectrometry (Q-TOF/MS) was coupled for the characterization of major compound. As (+)-nortrachelogenin was the most predominant compound in P. scabra Bunge, the quantification on it was also carried out with the method being validated. As a result, (+)-nortrachelogenin was found to be from 1.33 to 2.21 mg g −1 in this plant material. This rapid and effective analytical method could be employed for quality assessment of P. scabra Bunge, as well as pharmaceutical products containing this herbal material.