Objective To study the regulatory effects of long non-coding RNA HIF1A-AS1 on the myocardial ischemia reperfusion (I/R) injury and the related mechanism. Methods Myocardial I/R injury model was established with SD rats, and hypoxia reoxygenation (H/R) model was established with rat cardiac myocytes. si-HIF1A-AS1 was used to inhibit HIF1A-AS1 expression in the cardiac myoctyes. Then the mRNA expression of HIF1A-AS1 was detected by real-time PCR, the growth vitality of cardiac myocytes was investigated by MTT assay, the concentration of lactate dehydrogenase (LDH) in the culture media was detected by ELISA, and the autophagy-associated protein Beclin-1 expression was observed by Western blotting analysis. Results HIF1A-AS1 expression was increased in cardiac muscle of rat I/R model and rat cardiac myocytes of H/R model. Inhibition of HIF1A-AS1 by siRNA protected the cardiomyocytes against H/R injuries, reversing the decreased growth vitality of cardiac myoctyes, increased LDH level in the culture media, and increased expression of autophagy-related protein Beclin-1 induced by H/R stimulation. Conclusion Inhibition of long non-coding RNA HIF1A-AS1 might play a protective role in I/R injury of cardiac myoctyes by inhibiting the excessive autophagy of cardiomyocytes.