We aimed to evaluate the effect of melatonin on myocardial cell oncosis in the myocardial ischemia/reperfusion injury rat, and the role of the mitochondrial permeability transition pore (MPTP) therein. Sprague Dawley rats (N = 60) were randomly divided into five groups of 12 rats each: control, ischemia/reperfusion (I/R), melatonin treatment (MT), melatonin treatment + atractyloside (MT+ATR), and atractyloside (ATR). We prepared the myocardial ischemia/reperfusion model by reperfusion after the left anterior descending coronary artery was ligated for 30 min. The MT rats were given a 10 mg/kg MT intravenous injection immediately thereafter; the MT+ATR rats were also given a 5 mg/kg ATR intravenous injection 15 min before the ischemia; the ATR rats were given the ATR injection only. After 2-h reperfusion, myocardial tissue was extracted, the infarction size was determined, and myocardial ultrastructures were observed using electron microscopy. The expression level of the pre-oncosis receptor (porimin), which can induce membrane injury, was determined by western blot; the nicotinamide adenine dinucleotide (NAD(+)) content was determined spectrophotometrically. The four treatment groups showed upregulated expression of myocardial porimin, increased myocardial infarction size, and reduced NAD(+) content (P < 0.05). Compared with the I/R and MT+ATR groups, MT rats showed downregulated expression of myocardial porimin, reduced myocardial infarct size, and increased myocardial cell NAD(+) content (P < 0.05). The above indices between the ATR and MT+ATR groups were not significantly different (P > 0.05). Thus, MT might protect myocardial ischemia/reperfusion rats by inhibiting MPTP opening and reducing myocardial cell oncosis.