Abstract： There is a lack of syndrome differentiation methods in the existing system of Chinese medicine that can reflect the evolution of pathogenesis of chronic diseases，while cold damage，external contraction and warm febrile disease have theories and methods of staging syndrome differentiation，such as six-collateral syndrome differentiation and wei-qi-ying-blood syndrome differentiation， which can reflect rules of transmission and change of pathogenesis and predict its development. "All diseases result from qi disorder" and "prolonged diseases involving the collaterals” are the general principles of the theory of qi diseases and collateral diseases， which reveal the general mechanisms of disease occurrence and evolution. Therefore，the "qi-collateral syndrome differentiation" method based on the theory of qi diseases and collateral diseases can guide the staging or phased syndrome differentiation and treatment of chronic diseases. At the same time， qi-collateral syndrome differentiation also provides theoretical basis and treatment methods for Chinese medicine to treat disease before it arises，differentiation and treatment of functional diseases， early reversal of chronic diseases， and interruption of progression. This article explores the occurrence and evolution of diseases from the perspectives of Chinese medicine etiology and pathogenesis， combining the theories of qi diseases and collateral diseases. It analyzes the pathogenesis connotations of "all diseases result from qi disorder" and "prolonged diseases involving the collaterals"，and elaborates on the clinical guidance significance of qi-collateral syndrome differentiation in the staging diagnosis and treatment of chronic diseases in Chinese medicine.