Ischemic heart disease (IHD) is the leading cause of death worldwide. Although coronary intervention has significantly improved the prognosis of patients with obstructive coronary heart disease, nearly three-quarters of patients with angina pectoris are diagnosed with ischemia with non-obstructive coronary artery disease (INOCA). Among these, coronary microcirculation dysfunction (CMD) is the primary mechanism underlying angina pectoris and myocardial ischemia in INOCA patients, accounting for approximately two-thirds of all INOCA cases. Notably, the prevalence rate in women (ranging from 56% to 82%) is significantly higher than that in men. CMD is not only closely associated with adverse cardiovascular events such as heart failure, myocardial infarction, and sudden cardiac death, but also contributes to the development of coronary atherosclerosis. Additionally, it leads to a decline in patients’ quality of life, with nearly half of CMD patients experiencing anxiety and depression. However, only less than 7% of CMD patients in China receive appropriate treatment, highlighting prominent challenges in diagnosis and management. Based on the latest research progress, this article systematically reviews the multi-mechanistic pathogenic basis, non-specific clinical manifestations, diagnostic difficulties, and current treatment status of CMD. It aims to provide references for clinical precise diagnosis and treatment, and clarify the future research directions in this field.