Myocardial ischemia reperfusion (MI/R) injury is a severe pathological process that threatens human health all over the world. The role of microRNAs (miRNAs) in the pathogenesis of MI/R injury has been increasingly recognized in recent years. Here, we conducted a miRNA profiling of the hearts of MI/R injured rat model, and identified 46 miRNAs which were differentially expressed between the MI/R injury and the control groups. With a special focus on one of the most significantly changed miRNA, miR-30c-5p, we demonstrated its protective role against cardiomyocyte injury in tBHP-treated H9c2 cells. Overexpression of miR-30c-5p increased cell viability, decreased LDH release, and reduced cell apoptosis of cardiomyocytes after tBHP stimulation, accompanied with downregulated p53 expression. Noticeably, the level of miR-30c-5p was markedly upregulated in MI/R injury cells treated with panax notoginseng saponins (PNS), a traditional Chinese Medicine with significant clinical effects in the treatment of human MI/R injury. Moreover, miR-30c-5p inhibitor is sufficient to block the protection of PNS, as well as its active ingredient ginsenoside Re, against tBHP induced cardiomyocyte injury. The expression of p53 protein was also reduced in PNS treated cells. In summary, our study identified novel miRNA hits of MI/R injury, revealed a pivotal role of miR-30c-5p in cardiomyocyte damage and apoptosis after MI/R, and illustrated a miR-30c-5p-dependent therapeutic mechanism of PNS of this pathologic process. Future studies are warranted to examine the endogenous significance of miR-30c-5p, along with multiple other miRNA hits, in the pathogenesis and treatment of MI/R injury.