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Safflower Injection is one kind of injections derived from traditional Chinese medicine. It is widely applied to treat cerebrovascular diseases such as acute cerebral infarction, stroke, coronary heart disease, and angiitis. However, most adverse reactions of Safflower Injection in clinic are caused by its quality problems. In this study, 10 batches of normal and 42 batches of abnormal Safflower Injections were obtained from the clinical practice. Their quality fluctuations were detected by chemical fingerprinting (CF, ultra-performance liquid chromatography tandem mass spectrometry) and bioassays including cell-based biological profile (CBP) assay and enzymatic assay. CF identified 33 compounds in the Safflower Injections, and scutellarin and kaempferol-3-O-rutinoside were identified to be the possible components responsible for clinical adverse reaction. In addition, 59.5% (25/42), 85.7% (36/42) and 38.1% (16/42) of abnormal samples could be identified by CF, CBP assay and enzymatic assay, respectively. Interestingly, further integration of the three methods could entirely identify all the abnormal samples. It indicated that it is advisable to integrate CF, CBP assay and enzymatic assay for developing quality standard of Safflower Injections.