Abstract: Yin-Yang theory is one of the core components of the foundational theory of traditional Chinese medicine (TCM), yet its classification as philosophical or scientific has long been controversial. To move beyond the longstanding either-philosophy-or-science debate surrounding Yin-Yang theory in TCM, this article, for the first time, proposes a three-level framework spanning macro, meso, and micro perspectives. At the macro level, Yin and Yang are a theoretical achievement of ancient Chinese natural philosophy, used to explain universal laws governing how the cosmos operates, which constitutes Yin-Yang theory in philosophy; at the meso level, Huangdi Neijing (《黄帝内经》, Inner Canon of Huangdi) translated Yin-Yang from a cosmological framework into medical discourse, making it a core methodological basis for clinical pattern differentiation and treatment, which constitutes Yin-Yang theory in medicine; at the micro level, Yin-Yang theory in TCM has increasingly converged with modern science, showing scientific features that are testable and reproducible, which constitutes Yin-Yang theory in science. The article further demonstrates that Yin-Yang theory in TCM differs markedly from Yin-Yang as a general philosophical doctrine in core application and practical orientation: in the course of its medical transformation, elements related to life phenomena were selectively incorporated, while, within a medical context, abstract propositions such as cosmological speculation were bracketed and rendered concrete, thereby achieving a practice-oriented transition from philosophy to medicine. Based on this, the present study conducts analyses from four aspects, namely philosophical roots, clinical application, modern scientific interpretation, and implications for life sciences; it substantiates the logical basis for Yin-Yang theory in TCM as the overarching framework for clinical pattern differentiation and treatment, reviews modern research progress from perspectives such as systems science and network regulation, and explores its potential value in advancing a new paradigm of state-based medicine. The study suggests that an accurate understanding of Yin-Yang theory in TCM requires moving beyond the either-philosophy-or-science binary and analyzing specific issues on a case-by-case basis. Across different perspectives, Yin-Yang theory in TCM has philosophical, medical, and scientific attributes. Only by grounding the theory in actual clinical efficacy and engaging with modern science can the innovative development of Yin-Yang theory in TCM be promoted, thereby providing valuable Eastern insights for building a life science system with original Chinese contributions.