Acute myocardial infarction is the most common and aggressive type of human coronary disease. Red ginseng is a traditional Chinese medicine that is frequently used in formulae for the treatment of myocardial infarction. Although several network pharmacology methods have been developed to delineate the underlying pathophysiological pathways of traditional Chinese medicine in recent decades, very limited progress has been achieved in regard to interpretation because the veracity of these virtual prediction methods is largely limited due to inaccurate network models. Thus, we introduce a time-sequenced network analysis method based on a gene ontology interaction network to address the challenge of clarifying the precise pathway mechanism of a multicomponent complex biosystem. This time-sequenced gene ontology network indicates that the initial mechanism by which red ginseng treats myocardial infarction involves increasing the expression of insulin--like growth factor and glucocorticoid receptor in the ischaemic heart. Further experimental validation confirmed the antiapoptotic effect of ginseng through the induction of the expression of myocardial insulin--like growth factor and the side effects of increasing the expression of glucocorticoid receptors in a myocardial infarction mouse model. Therefore, we explored an effective time-sequence network analysis method that is feasible for elucidating the major pharmacological mechanisms of complex multidrug biosystems, such as Chinese medicine.