Safflower is a popular Chinese medicinal plant and Safflower injection is extensively used for the clinical treatment of cerebrovascular and cardiovascular diseases. In this study, HPLC-DAD-ESI-MSn was utilized to study the stability and degradation of the two major but chemically unstable bioactive compounds hydroxysaffior yellow A and anhydrosaffior yellow B, in Safflower injection. The impact of light irradiation, temperature, and pH on the stability of these two compounds were studied. The results showed that hydroxysafflor yellow A and anhydrosafflor yellow B could degrade at high temperature (〉60 ℃) or extreme pHs (pH ≤ 3.0 or 〉7.0), but not under light irradiation. The common degradation product was p-coumaric acid. Chemical structures of the other degradation products were characterized by LC-MS. Hypothetical degradation pathways were proposed. In addition, ADP-induced platelet aggregation tests showed that the degradation of anhydrosaffior yellow B could reduce the anticoagulation activities of Safflower injection. Our results suggest that temperature and pH are critically important for the preparation and storage of Safflower injection.