Objective To investigate the effect of adipocytokine Apelin-13 (AP13) on mitochondrial autophagy in myocardial ischemia reperfusion injury (MIRI) and its mechanism. Methods MIRI model was established by ligating the coronary artery branches of rats. The rats are divided into sham group, AP13-treated sham group, MIRI group and AP13-treated MIRI group. 24 h after the establishment of MIRI model, serum creatine kinase (CK), lactate dehydrogenase (LDH) and cardiac troponin I (cTnI) levels were detected by ELISA, and the size of myocardial infarction was detected by 2, 3, 5-triphenyltetrazole chloride (TTC) staining. Terminal deoxynucleotidyl transferase mediated dUTP-biotin nick end labeling (TUNEL) was used to detect the apoptosis of myocardial cells in MIRI myocardium, and transmission electron microscopy (TEM) was employed to observe the mitochondrial damage of myocardial cells and the formation of autophagosomes in the damaged myocardium. Western blot analysis was used to detect the microtubule-associated protein 1 light chain 3 II (LC3 II)/LC3 I ratio and protein expression level of the ubiquitin-binding protein (P62), phosphatase and tensin homologous (PTEN)-induced kinase 1 (PINK1), E3 ubiquitin ligase parkin and cleaved-caspase-3(c-caspase-3)in myocardial infarction tissues of rats in each group. The myocardial cells isolated from myocardial infarction area of rats were infected with adenovirus carrying GFP-LC3, and the co-localization of translocase of outer mitochondrial membrane 20 (TOM20) and LC3 was observed by immunofluorescence cytochemical staining. Results Compared with sham operation group or AP13-treated sham group, serum CK, LDH, cTnI, myocardial infarction area and apoptosis rate of MIRI group or AP13-treated MIRI rats were significantly increased, and there was no significant difference between the first two groups. Compared with MIRI group, the above changes were significantly decreased in AP13-treated MIRI rats. The integrity of mitochondrial structure in cardiomyocytes was significantly damaged, and a large number of autophagosomes enclosing mitochondria appeared in MIRI group and AP13-treated MIRI group compared with the sham group or AP13-treated sham group. However, compared with MIRI group, mitochondrial damage of myocardial cells in AP13-treated MIRI group was significantly reduced, and the number of autophagosomes was significantly increased. LC3 II/LC3 I ratio, PINK1, parkin and c-caspase-3 protein expression were significantly increased, while the expression level of P62 was significantly decreased in MIRI group or AP13-treated MIRI group compared with the other two groups. The change trend of above protein levels in AP13-treated MIRI group was significantly decreased compared with MIRI group. LC3 and TOM20 were co-located in the mitochondria of cardiomyocytes after MIRI modeling, and the expression intensity of LC3 in AP13-treated MIRI group was significantly increased compared with that in MIRI group. Conclusion Aplein-13 may promote the level of mitochondrial autophagy through PINK1/parkin signaling pathway, which can effectively reduce the size of myocardial infarction caused by I/R and reduce the rate of apoptosis.