The morphological appearance and main ingredients of three Chinese medicines (CMs), P. ginseng, P. quinquefolius, and P. notoginseng of the Panax genus, are similar. However, their pharmacological activities are obviously different. To ensure their safety and efficacy, chemical characteristics of the three CMs were determined using pressurized liquid extraction and HPLC-evaporative light scattering detection. Twelve major saponins, namely notoginsenoside R1, pseudo-ginsenoside F11, ginsenosides Rg1, Re, Rf, Rb1, Rg2, Rc, Rb2, Rb3, Rd, and Rg3 were also quantitatively compared among the three CMs. The contents of total investigated saponins varied considerably, by up to 4-14-fold, between the highest (P. notoginseng, 82.8-136.5 mg/g) and the lowest values (P. ginseng, 10.0-21.1 mg/g). Hierarchical clustering analysis based on the characteristics of 11 investigated saponins (except ginsenoside Rb3) and notoginsenoside R1, pseudo-ginsenoside F11, and the ratio of ginsenoside Rg1/Rb1 and Rg1/Re showed that 56 tested samples were divided into three main clusters in accordance with the three Panax species. Similarity evaluation of chromatograms was also performed using "Similarity Evaluation System for Chromatographic Fingerprint of Traditional Chinese Medicine (Version 2004A)". The results showed that a high degree of similarity existed within individual clusters, but a low degree between the clusters, which could be used for quality control of the three CMs.