This paper discussed Professor Shi Qi’s academic thoughts of prevention and treatment of bone metabolic diseases. Through the clinical and fundamental research,he considers the pathological basis of bone metabolic diseases as deficiency of kidney essence,imbalance of yin and yang and bone loss due to essence deficiency,and creates the therapy principle of invigorating kidney for nourishing essence and harmonizing kidney yin and yang, proposes a series of research programs,techniques and guidelines in clinic. He elaborates that the therapy of invigorating kidney for nourishing essence plays a role in the prevention and treatment of bone metabolic diseases through recovering the balance between osteoblast mediated bone formation and osteoclast mediated bone resorption and maintaining bone homeostasis,which are taken as the development of theory of “kidney governing bones”“kidney storing essence” and further expand the guiding role of theory of traditional Chinese medicine in clinical practice and fundamental research.