Traditional Chinese Medicine diagnosis and treatment principles, established through centuries of trial-and-error clinical practice, directly maps patient-specific symptom patterns to personalised herbal therapies. These empirical holistic mapping principles offer valuable strategies to address remaining challenges of reductionism methodologies in modern biomedicine. However, the lack of a quantitative framework and molecular-level evidence has limited their interpretability and reliability. Here, we present an AI framework trained on ancient and classical TCM formula records to quantify the symptom pattern-herbal therapy mappings. Interestingly, we find that empirical TCM diagnosis and treatment are consistent with the encoding-decoding processes in the AI model. This enables us to construct an interpretable TCM embedding space (TCM-ES) using the model's quantitative representation of TCM principles. Validated through broad and extensive TCM patient data, the TCM-ES offers universal quantification of the TCM practice and therapeutic efficacy. We further map biomedical entities into the TCM-ES through correspondence alignment. We find that the principal directions of the TCM-ES are significantly associated with key biological functions (such as metabolism, immune, and homeostasis), and that the disease and herb embedding proximity aligns with their genetic relationships in the human protein interactome, which demonstrate the biological significance of TCM principles. Moreover, the TCM-ES uncovers latent disease relationships, and provides alternative metric to assess clinical efficacy for modern disease-drug pairs. Finally, we construct a comprehensive and integrative TCM knowledge graph, which predicts potential associations between diseases and targets, drugs, herbal compounds, and herbal therapies, providing TCM-informed opportunities for disease analysis and drug development.