UNLABELLED: With thousands of years of application history, traditional Chinese medicine (TCM) has unique advantages in the prevention of various chronic diseases, and in recent years, the development of TCM has presented a situation where opportunities and challenges coexist. Phenomics is an emerging area of life science research, which has numerous similarities to the cognitive perspective of TCM. Thus, how to carry out the interdisciplinary research between TCM and phenomics deserves in-depth discussion. Diabetes is one of the most common chronic non-communicable diseases around the world, and TCM plays an important role in all stages of diabetes treatment, but the molecular mechanisms are difficult to elucidate. Phenomics research can not only reveal the hidden scientific connotations of TCM, but also provide a bridge for the confluence and complementary between TCM and Western medicine. Facing the challenges of the TCM phenomics research, we suggest applying the State-target theory (STT) to overall plan relevant researches, namely, focusing on the disease development, change trends, and core targets of each stage, and to deepen the understanding of TCM disease phenotypes and the therapeutic mechanisms of herbal medicine. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-023-00146-6.