As an important part of Chinese civilization, traditional Chinese medicine (TCM) has a long history and broad social foundation. In the development of modern medicine, TCM bears the responsibility of inheriting Chinese culture, while integrating with modern science and technology to continuously promote medical progress. The theory of “state‐target differentiation and treatment” is an innovative model combining Chinese and Western medicine that has provided a new mindset and method for modernizing TCM. This theory not only guides the reconstruction of modern TCM diagnosis and treatment systems, but also strongly promotes the reconstruction of the modern herbal system. As an emerging bioinformatics technology, phenomics research can reveal biological processes dynamically and quantitatively, which will help “open the black box” of TCM by providing technical methods to reveal the nature of “state” and the mechanism of “state modulation” in TCM. TCM can provide a valuable clinical reference from the perspective of disease cognition, sort out phenomics information parameters systematically and uniformly, and provide more accurate and meaningful data for phenomics research. The in‐depth combination of TCM and phenomics from the concept and technology will vigorously promote the development of human precision medicine. Modern TCM research guided by the theory of state‐target differentiation and treatment can effectively improve the scientific basis and targetability of clinical treatments and can also initiate a breakthrough in the integration of Chinese and Western medicine, further promoting the profound communication and cooperation between Chinese and Western medicine, so as to achieve better development of medicine in the future.