Root of Panax notoginseng (Sanqi in Chinese) is a highly valued and commonly used Chinese medicine. It has been widely used for treatment of cardio- and cerebro-vascular diseases. In this study, a method involving human platelet extraction and HPLC-DAD-ESI-MS/MS was developed for screening potential anti-platelet aggregation agents in Sanqi. Five compounds which could interact with human platelets were found, and four were identified as adenosine, guanosine, ginsenoside Rh1, and ginsenoside F1, respectively. The effects on rabbit platelet aggregation induced by arachidonic acid, adenosine diphosphate, and thrombin were also investigated in vitro. The results showed that the nucleosides adenosine and guanosine mainly contributed to the anti-platelet aggregation of Sanqi. The data suggest that human platelet extraction combined with HPLC-DAD-ESI-MS/MS is a useful method for screening anti-platelet aggregation agents from Chinese medicines.