Based on the duality of "healthy" and "pathogenic" of the immune system in physiological and pathological states， and combined with the analogy between "immune function" and "healthy qi"， the theory of "transformation of healthy qi into pathogenic qi" was proposed to guide the pattern identification and treatment of autoimmune diseases. The theory of "transformation of healthy qi into pathogenic qi" means that "healthy qi"， which is originally used by the body's original ability to defend and remove harmful factors or normal functional activities， transformed into "pathogenic qi"， which is factors that damage and destroy the human body or abnormal body state. In the pathogenesis of autoimmune diseases， the pathogenic factors and causes of congenital endowment， tissue damage under the influence of external pathogens， abnormal function of zang-fu （脏腑） organs and meridians， abnormal transmission and transformation of qi， blood， body fluids was proposed. Autoimmune diseases have the dynamic mechanism of latent pathogen at early stage， internal and external contraction at the onset stage， and the expansion of the pathogenic qi at the complete period， and also have the characteristics of the specificity， invisibility and contradiction of healthy qi and pathogenic qi. In terms of treatment， it advocates the ideas of treatment with both attack and supplementation throughout the disease， identifying diseases with special prescriptions and formulas for specific diseases， dynamically adjusting treatment by identifying the remission and onsets of the disease， observing the changes in the dynamics of healthy qi transforming into pathogenic qi， and treating disease before it arises with early intervention.