Coronary microcirculation disorder after myocardial ischemia reperfusion （MIR） is a prominent problem in the treatment of coronary heart disease. According to the physiological commonality between “collaterals-sweat pore qi and fluid” and coronary microcirculation， and the evolution of the course of MIR， it is believed that “heart collateral stasis obstruction， sweat pore constraint and block” is the cause of coronary microcirculation disorder. The evolution of the pathogenesis can be divided into three periods. During the myocardial ischemia period， the pathogenesis is heart collaterals obstruction and sweat pores empty， while during the ischemia reperfusion period， it is internal formulation of deficiency wind， spasms of collaterals or slight heart collaterals obstruction； in the coronary microcirculation disorder period， sweat pores constraint and block， constraint transforming into heat， qi and fluid failing to diffuse are the pathogenesis. The corresponding treatment principle is assisting dredge with supplementation， and supplementing deficiency to dispel stasis； treating wind and blood simultaneously， and extinguishing wind to arrest convulsion； clearing heat and cooling blood， and diffusing qi and unblocking qi and fluid. Moreover， it is recommended to treat the heart and lungs simultaneously， and regulate the heart and liver at the same time.