Fructus Psoraleae, a widely used traditional Chinese medicine, is well known as a health supplement ingredient. In our study, an improved and comprehensive HPLC fingerprint of Fructus Psoraleae was established. Two important new benzofuran glycosides, psoralenoside and isopsoralenoside, were identified as characteristic constituents for the first time. HPLC separation was performed on an RP-C8 column. The mobile phase was acetonitrile and 0.1% acetic acid solution with linear gradient change of acetonitrile from 10 to 82% in 40 min. The flow rate was 1.0 mL/min, and the detection wavelength was set at 310 nm. The HPLC chromatograms of twenty-six samples from different regions of China showed a similar pattern. Twelve peaks were selected as characteristic peaks and further identified as psoralenoside, isopsoralenoside, psoralen, isopsoralen, bavachromene, corylifolin, corylin, psoralidin, isobavachalcone, bavachinin, corylifol A, and bakuchiol, respectively. Nine of them were simultaneously quantitatively analyzed for the first time. A more comprehensive analytical method was established for the fingerprint of Fructus Psoraleae. It is very useful for authentication and quality assessment of the crude drug.