The adverse drug reaction (ADR) of traditional Chinese medicine injection (TCMI) has become one of the major concerns of public health in China. There are significant advantages for developing methods to improve the use of TCMI in routine clinical practice. The method of predicting TCMI-induced ADR was illustrated using a nested case-control study in 123 cases and 123 controls. The partial least squares regression (PLSR) models, which mapped the influence of basic characteristics and routine examinations to ADR, were established to predict the risk of ADR. The software was devised to provide an easy-to-use tool for clinic application. The effectiveness of the method was evaluated through its application to new patients with 95.7% accuracy of cases and 91.3% accuracy of controls. By using the method, the patients at high-risk could be conveniently, efficiently and economically recognized without any extra financial burden for additional examination. This study provides a novel insight into individualized management of the patients who will use TCMI.