Aim To study the protective effect of trimetazidine (TMZ) on mitochondria of myocardial ischemia and ischemia reperfusion injury and its mechanism. Methods Totally 50 SD rats were randomly divided into 4 groups: the pseudooperation group, the saline group and the TMZ treated groups (5 mg/kg and 10 mg/kg). In the pseudooperation group the coronary artery was not ligated but the chest was opened, the other groups were the model of myocardial ischemia reperfusion injury(RI). The level of malonaldehyole(MDA), superoxide dismutase (SOD), glutathione (GSH), glutathione peroxidase (GSH-Px) and the accumulation of Ca 2+ in mitochondria of myocardial were detected at ischemia 30 min and reperfusion 40 min. The myocyte ultrastructure was also observed by electron microscope in 4 groups. Results Compared with the pseudooperation group, the MDA and total Ca 2+ were significantly higher and the SOD, GSH, GSH-Px were significantly lower in saline group and treated groups. Compared with the saline group, the MDA and total Ca 2+ was significantly lower and the SOD, GSH, GSH-Px were significantly higher in treated group. The ultrastructure changes of myocardium ulder electron microscope showed that the damage degree of mitochondria is slighter in TMZ treated groups than in saline group. Conclusions TMZ could significantly reduce the injury of lipid peroxidation of myocardial mitochondrial induced by ischemia and ischemia reperfusion. The mechanism may be that TMZ could increase the content of GSH and the acvitity of SOD and GSH-Px, and enhance its antioxidant production. TMZ could protect the cardiac cells by reducing calcium overload in myocardial mitochondria.