Objective To investigate the effect of targeted inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9) on myocardial ischemia-reperfusion injury (MIRI) in rats and explore its mechanism of action. Methods A MIRI model was established using clean-grade 8-week-old male SD rats. Forty rats were randomly divided into sham group, model group, shPCSK9 group, and PCSK9 inhibitor group, with 10 rats in each group. One week and 30 minutes before surgery, the shPCSK9 group was injected with shPCSK9 lentivirus through the tail vein, the PCSK9 inhibitor group was injected with PCSK9 inhibitor subcutaneously. The sham operation group and the model group were injected with an equal amount of normal saline. Enzyme-linked immunosorbent assay (ELISA) method was used to determine the levels of serum lactate dehydrogenase (LDH), creatine kinase isoenzyme (CK-MB) and cardiac troponin I (cTnI) in the rats of each group. Hematoxylin-eosin (HE) staining was used to observe the myocardial histological changes of the rats in each group. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining was used to observe the apoptosis of myocardial cells in the rats in each group. Tissue immunofluorescence staining was used to detect the expression of lysosomal-associated membrane protein (LAMP)2 protein in the myocardial tissue of the rats in each group. Western blot was used to detect the protein expressions of PCSK9, microtubule-associated protein 1 light chain 3 (LC3)Ⅱ/LC3Ⅰ, p62, autophagy-related gene 5 (ATG5), transcription factor EB (TFEB), LAMP1, LAMP2, cathepsin D (CTSD) and nuclear TFEB in the myocardial tissues of the rats in each groups. Results Compared with the sham operation group, the levels of CK-MB, cTnI and LDH in the serum of rats in the model group were increased, myocardial cells and myocardial fibers were significantly damaged, the TUNEL positive rate in myocardial tissue was increased, the LAMP2 positive expression area was reduced, the relative protein expression levels of PCSK9 and p62 were upregulated, the LC3Ⅱ/LC3Ⅰ protein ratio and the relative protein expression level of ATG5 were downregulated, and the relative protein expression levels of TFEB, LAMP1, LAMP2, CTSD and the relative protein expression level of nuclear TFEB were all downregulated (all P＜0.05). Compared with the model group, the levels of CK-MB, cTnI and LDH in the serum of rats in the shPCSK9 group and the PCSK9 inhibitor group were reduced, the pathological damage of myocardial cells and myocardial fibers was alleviated, the TUNEL positive rate was reduced, the LAMP2 positive expression area was increased, the relative protein expression levels of PCSK9 and p62 were downregulated, the LC3Ⅱ/LC3Ⅰ protein ratio and the relative protein expression level of ATG5 were upregulated, and the relative protein expression levels of TFEB, LAMP1, LAMP2, CTSD and the relative protein expression level of nuclear TFEB were also upregulated (all P＜0.05). Conclusion Targeted inhibition of PCSK9 may reduce myocardial cell apoptosis and damage by activating TFEB-mediated lysosomal function and improve MIRI in rats