Vitexin (VT) is a main bioactive flavonoid compound derived from the dried leaf of hawthorn (Crataegus pinnatifida), a widely used Chinese traditional folk medicine. Recent studies have shown that vitexin presents cardioprotective effects in vivo and in vitro. Mitochondrial dysfunction is a salient feature of myocardial ischemia/reperfusion (I/R) injury (MIRI), but the potential mechanism is still unclear. This study investigated the cardioprotective effect of vitexin against MIRI and its possible mechanism. Isolated SD rat hearts were subjected to MIRI in a Langendorff perfusion system, and H9c2 cells were subjected to hypoxia/reoxygenation (H/R) in vitro. Ex vivo experiments showed improved left ventricular function and reduced infarct size in the vitexin group. Transmission electron microscopy showed that I/R caused outer mitochondrial membrane rupture, cristae disappearance and vacuolation, while vitexin reduced mitochondrial damage and ultimately reduced cardiomyocyte apoptosis. In vitro, vitexin protected H9c2 cells from H/R-induced mitochondrial dysfunction, significantly reducing ROS levels; improving mitochondrial activity, mitochondrial membrane potential and ATP content; markedly increasing MFN2 expression and reducing the recruitment of Drp1 in mitochondria. These results suggest a new protective mechanism of vitexin for ischemic heart disease treatment.