Coronary microembolization (CME) occurs in patients with acute coronary syndrome and is caused primarily by atherosclerotic plaque rupture associated with surgery. CME can lead to arrhythmias, decreased coronary blood flow reserve, and cardiac systolic dysfunction. The clinical efficacy of conventional coronary artery dilation, antiplatelet agents, and direct thrombus aspiration after CME is not satisfactory. Studies have indicated that microRNAs (miRNAs) specifically bind the 3′ untranslated regions (UTRs) of inflammatory response-, apoptosis-, and autophagy-related mRNAs, and ultimately affect CME prognosis. In-depth studies of the roles of miRNAs in CME occurrence and development would not only advance understanding of the mechanisms underlying poor prognosis after CME but also aid in identifying new targets for drug treatment. Here, we review the regulatory effects of miRNAs on myocardial cell injury after CME in terms of the inflammatory response, apoptosis, and autophagy. Overall, changes in miRNA levels after CME decrease myocardial autophagy and worsen cardiac prognosis. Current evidence suggests a potential strategic pathway for therapeutic intervention in CME management.