Abstract: The theory of traditional Chinese medicine (TCM) is fundamentally grounded in a holistic perspective, wherein the properties and effects of crude drugs illustrate its action mechanisms at different levels. However, a notable discrepancy persists between the traditional theory of drug properties and modern research on drug efficacy, highlighting the need for interdisciplinary approaches to elucidate their scientific connections. This article reviews research approaches and case studies that utilize systems biology methods to analyze the core network and key modules of drug properties, as well as employ chemical biology techniques to elucidate the interaction mechanisms between active components and their targets. Herein, a chemobiological research paradigm integrating systems theory with reductionism was proposed, leveraging the unique advantages of TCM and its properties and effects. By integrating molecular probe tracing and identification, multi-omics analysis, network prediction, and dynamic regulatory network interpretation of drug properties, this approach overcomes the limitations of single-target or efficacy research and establishes a framework for mutual validation between "the whole" and "the part". The dual methodology serves as a critical entry point for tackling medical challenges, facilitating a transition from observing phenomena to uncovering essence and from dealing with ambiguity to achieving precision. This approach effectively illuminates the fundamental nature of the medicinal properties and pharmacodynamic effects. Simultaneously, by refining the evaluation system for TCM property theories and constructing a "properties-effects-compositions" correlation framework, the bottleneck in quality control of TCM can be effectively addressed, thereby highlighting the critical role of chemical biology in driving innovative research in TCM.