According to statistics, 67% women and 33% men with angina and 10% of patients with acute myocardial infarction have no significant stenosis in the epicardial coronary lumen during coronary angiography (CAG). After excluding coronary spasm, thrombosis autolysis, mental and other factors, no significant stenosis was found in CAG but the patients still had symptoms of myocardial ischemia, suggesting the existence of coronary artery microcirculation disorder (CMD). The CMD mechanism is still unclear, and it is generally believed that the main mechanisms leading to CMD are coronary microembolization (CME), endothelial dysfunction (ED), myocardial ischemia/reperfusion injury (MIRI) and autonomic dysfunction (AD). A large number of non-coding RNA (ncRNA) are involved in the development of CMD through these mechanisms. This review focuses on the regulatory role of microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA) in the development and treatment of CMD.