Knowledge of signal transduction pathways and their corresponding signaling molecules is critical in evaluating potential therapeutic targets. Traditional Chinese Medicine (TCM) used Yang and Yin to describe the physiological processes in human body, but its scientific basis is unknown. According to “Yellow Emperor’s Inner Canon” (YEIC)―the fundamental doctrinal source for TCM―there are five elements of Yang-Yin, each pertaining to particular physiological functions. Their interaction and relationship determine the physiological conditions of human being. In this work, iterative selection method was used to correlate YangYin-Qi with signal molecules. It is revealed that the signal transduction pathways are identical to the dialectical relationships of Yang-Yin-Qi(s). With the direct mapping between Yang-YinQi(s) and signaling molecules, the signal transduction pathways are consistent with TCM therapeutic strategies too. In addition, it is demonstrated that the Chinese herbal medicine regulates signal transductions. With the correlation between Yang―Yin(s) and signal transduction pathways, it is evident that the modern medicine and TCM identified the same pathogenesis of diseases, such as hematuria, constipation, hemorrhoidal disease, nocturnal enuresis, frequent urination, gall stone, acute cholecystitis and hypertension, etc; with highly similar treatment strategy, albeit using different terminologies.