Objective  To investigate the protective effect of micro RNA(miR)-98-5p targeting Kruppel-like factor 9(KLF9) against myocardial ischemia-reperfusion(MI/R) injury in rats.   Methods  Totally 50 rats were randomly divided into sham operation group, model group, miR-98-5p agomir group, agomir-NC group, and miR-98-5p agomir+pcDNA-3. 1-KLF9 group, 10 in each group. MI/R model was established by coronary artery ligation. The pathological changes of myocardial tissue were detected by HE staining. The myocardial apoptosis were detected by TUNEL. The levels of creatine kinase (CK), creatine kinase isoenzymes (CK-MB) and lactate dehydrogenase (LDH) in serum were detected by ELISA. The expression levels of miR-98-5p and KLF9 mRNA were detected by Real-time PCR. The expression of KLF9, Bax and JAK2/STAT3 pathway relative protein were detected by Western blotting. Dual luciferase assay verified the relationship between miR-98-5p and KLF9.  Results  Compared with the sham operation group, the arrangement of myocardial cells in the model group was disordered, and the myocardial cells appeared necrosis. The apoptosis rate of myocardial cells, serum CK, CK-MB and LDH contents increased, the expression level of miR-98-5p decreased, and the expression levels of KLF9 mRNA and protein, p-JAK2 and p-STAT3 protein increased (P<0.05). After the overexpression of miR-98-5p, the myocardial cells arranged more orderly and the myocardial cell necrosis decreased. The apoptosis rate of myocardial tissue, the contents of CK, CK-MB and LDH in serum and the expression of p-JAK2 and p-STAT3 protein were decreased (P<0.05). The result  of dual luciferase assay showed that KLF9 was the target gene of miR-98-5p. The overexpression of KLF9 reversed the effects of miR-98-5p agomir on myocardial injury.  Conclusion  MiR-98-5p targeting KLF9 can improve the myocardial injury of MI/R rats. The mechanism may be related to the regulation of JAK2/STAT3 signal pathway by miR-98-5p which inhibit myocardial cell apoptosis.