Herbal injection is one of the most powerful preparations of modern Traditional Chinese Medicine; however the quality control of it is fairly difficult for their complicated constituents. Recently, chromatographic fingerprint (CF) has been recommended as a potential strategy for the quality control of herbal injection, nevertheless there are still various substances absent from the inspection of chromatographic method for no spectrum absorption, which might cause grievous drug-induced disease. To establish a comprehensive and early prediction security control process, biothermodynamic fingerprint (BF) was adopted as a complement for CF to detection the quality fluctuation of herbal injection from both chemical and bioactive aspect. In this work, Yinzhihuang Injection (YZHI) was selected as a representative of herbal injection, 10 batches of normal samples and 6 batches of artificial abnormal samples were collected, high performance liquid chromatography and Thermal Active Monitor were applied to develop their CF and BF respectively. The results showed that the CF and BF of normal samples were similar with good stability and consistence; however the abnormal samples deviated from standards. All abnormal samples could be correctly distinguished when coupled CF with BF, the recognition ratio was higher than CF and BF respectively, and the key factors of quality fluctuation extent could be ordered as bacterial contamination, high temperature, lighting and sterilizing condition. The established method could be used for early prediction adverse drug events, which would be potentially helpful to improve the safety level of herbal injection in clinical application.