The prognosis of myocardial ischemia/reperfusion (I/R) injury is poor in elderly patients. Aging increases the susceptibility of the heart to cell death from I/R injury and prevents the optimal effectiveness of cardioprotective modalities. Since the interaction of aging with cardioprotection is multifactorial, combination therapy may overcome the above-mentioned burden through correcting various components of the injury. Here, we explored the effects of nicotinamide mononucleotide (NMN)/melatonin combination therapy on mitochondrial biogenesis and fission/fusion, autophagy, and microRNA-499 in the aged rat heart with reperfusion injury. Ex vivo model of myocardial I/R injury was established by coronary occlusion and re-opening in 30 aged male Wistar rats (400-450g, 22-24months old). NMN (100mg/kg/48h, intraperitoneally) was administered over 28days before I/R, and melatonin (50µM) was added to the perfusion solution at early reperfusion. CK-MB release and expression of mitochondrial biogenesis genes and proteins, mitochondrial fission/fusion proteins, autophagy genes, and microRNA-499 were assessed. NMN/melatonin combination therapy concomitantly decreased CK-MB release in aged reperfused hearts (P < .001). It also upregulated SIRT1/PGC-1α/Nrf1/TFAM profiles at both gene and protein levels, Mfn2 protein, and microRNA-499 expression, and downregulated Drp1 protein and Beclin1, LC3, and p62 genes (P < .05 to P < .001). The effect of combination therapy was greater than individual ones. Co-application of NMN/melatonin within the setting of I/R injury in the aged rat heart induced noticeable cardioprotection through modulation of a coordinated network including microRNA-499 expression along with mitochondrial biogenesis associated with SIRT1/PGC-1α/Nrf1/TFAM profiles, mitochondrial fission/fusion, and autophagy, therefore, appears to prevent the burden of myocardial I/R injury in elderly patients.