Objective To investigate the effect of fentanyl combined with propofol on cardiac autophagy and cardiac ischemia reperfusion injury (I/ R) in rats. Methods Thirty healthy male SPF SD rats were randomly divided into five groups: the sham group, model group, fentanyl group, propofol group and fentanyl+propofol group. The I/ R model was established for all groups except the sham group. The fentanyl group, propofol group and fentanyl+propofol treatment group were pretreated with 20 μg / kg fentanyl, 50 mg / kg propofol and 20 μg / kg fentanyl combined with 50 mg / kg propofol, respectively. After 30 min, the rats were sacrificed and heart tissue was collected for analyses. HE and TUNEL staining were used to observe the pathological injury of rat heart tissue, TTC staining was used to observe the area of myocardial infarction and electron microscopy was used to observe mitochondrial structure. Western blot was used to detect the expression of autophagy-related proteins Beclin1, ATG5 and L3B. Results Myocardial pathological changes were observed in the model group but not the sham group; in addition, the percentage of cardiac cell apoptosis and infarct area were increased, mitochondrial swelling in myocardial cells was observed and the expression of autophagy-related proteins Beclin1, ATG5 and L3B-II were increased. Treatment of 20 μg / kg fentanyl, 50 mg / kg propofol and 20 μg / kg fentanyl combined with 50 mg / kg propofol pretreatment significantly reduced myocardial pathological injury, cardiac apoptosis and percentage of infarct area in I/ R rats. The treatments alleviated mitochondrial swelling in myocardial cells and decreased the expression of autophagy-related proteins Beclin1, ATG5 and L3B-II. Pretreatment of 20 μg / kg fentanyl combined with 50 mg / kg propofol showed the best performance among the three treatments; there was no significant difference between fentanyl and propofol. Conclusions Both fentanyl and propofol inhibit autophagy, alleviate mitochondrial swelling and reduce myocardial I/ R injury. There was not a significantly different effect between 20 μg / kg fentanyl and 50 mg / kg propofol in the treatment of myocardial I/ R injury. In addition, the combination of fentanyl and propofol had a synergistic effect on myocardial I/ R injury.