Myocardial ischemia-reperfusion injury (MIRI) is one of the important causes of death in humans. Animal experiments and clinical studies have confirmed that ischemic preconditioning (IPC) has a clear cardioprotective effect, but the specific mechanism remains unclear. Mitochondria are the main site for the production of ATP by cardiomyocytes, and play an important role in maintaining energy metabolism and ion homeostasis in cardiomyocytes. Energy failure and mitochondrial permeability transition pore (mPTP) opening are considered to be the main cause of MIRI, and IPC ultimately plays a role in myocardial protection by improving mitochondrial structure and energy metabolism. Therefore, mitochondria are the main organelles for mitigating MIRI by IPC.With the development of research techniques such as omics and bioinformatics, a series of new experimental methods have been used to explore the mitochondrial mechanism about myocardial protection of IPC.Here we mainly introduce the mitochondria mechanism about channels, proteins, autophagy and genes ,which relate to mypcardial protection of IPC.