The theory of yin-yang is a foundational concept in traditional Chinese medicine (TCM) and has been refined through millennia of clinical practice and theoretical development. This theory remains central to syndrome differentiation and therapeutic decision-making. With rapid advances in modern biomedicine and information sciences, this review synthesizes recent interdisciplinary progress linking yin-yang concepts to cellular metabolism, redox balance, gene regulation, and immunomodulation. We outline how pathological states historically described as “yin deficiency” or “yang hyperactivity” correspond to alterations in cellular energy conversion, molecular signaling networks, and systemic homeostasis, and we critically evaluate current evidence for mechanistic pathways. Notwithstanding promising correlations, major gaps persist in mechanistic clarity and the establishment of quantitative metrics, limiting the rigorous integration of yin-yang theory into evidence-based frameworks. To address these gaps, we propose a research roadmap that leverages modern biotechnology, mathematical modeling, and artificial intelligence for quantitative multiscale analysis. By integrating molecular, cellular, and systemic datasets, this approach can clarify the biological connotations of yin-yang balance for physiology, disease mechanisms, and clinical outcome assessment.