Coronary microvascular disease(CMVD) is insidious in onset，deeply rooted，persistent，and triggered by various factors，sharing similarities with the latent pathogen characteristics of “latent，lingering，and dynamic”.From the perspective of the “latent pathogen”，this article explored the CMVD pathological progression of CMVD and proposed that the latent pathogen was essentially identical.During the onset of CMVD，“latent pathogens” often hide in the heart collateral and occur at a certain time，with “endogenic phlegm and stasis lurking in the heart collateral” being the basis of CMVD onset.The fundamental cause of disease lies in healthy qi deficiency and the inability to resist pathogenic factors.Pathogens hide in the heart collateral，remaining latent until triggered by exogenous and internal injuries during healthy qi deficiency.During the acute phase，the focus is on eliminating pathogen and relieving excess to facilitate the smooth flow of heart collateral，with resolving phlegm and dispelling stasis as methods.In the alleviation phase，the emphasis shifts to nourishing the spleen and kidney，supporting healthy qi，while medicines are mainly used for warming yang and replenishing qi，as well as nourishing yin and tranquilizing mind.In clinical practice，special attention should be paid to the rational use of medicines that disperse wind and dredge collaterals，such as insect and vine herbs.This paper emphasized the staged treatment of CMVD based on the “latent pathogen” theory and combined it with the CMVD pathogenesis progress.