Ischemia-reperfusion injury (I/RI) is the damage of tissues and organs resulting in different dysfunctions when ischemia and subsequent reperfusion process happen in heart surgery, organ transplantation and vascular diseases. Mitochondrial dysfunction is considered to be one of the important causes of I/RI, because mitochondria damage will lead to energy generation reduction, reactive oxygen species increase and calcium overload, thereby activating the process of cell death. Mitochondria is a highly dynamic organelle, which maintains autogenous homeostasis by fusing and dividing continuously. It has been proven that mitochondria can be transmitted between cells to improve the function of damaged tissues. With the maturity of organelle extraction technology, some scholars have been able to extract functional mitochondria. Therefore, mitochondrial transplantation (MT) appears in above context. The active mitochondria are firstly extracted and purified from healthy tissues, and then transplanted into damaged organs via local or vascular injections. The exogenous mitochondria may fuse with endogenous mitochondria or replace damaged mitochondria DNA after entering the cell by actin internalization. Tissue dissociation and differential filtration is an innovation from McCully’s team, it can separate 2×10¹⁰ high-purity functional mitochondria from 0.18 g fresh tissue in less than 30 min. Up to date, the treatment outcomes of MT on heart, brain, kidney, lung and liver acute I/RI have already been more explored. However, there are still many challenges in the clinical application of MT. First of all, there is no standardized transplantation procedure to confirm details, such as dose, mode and time. Secondly, the exact mechanism on MT’s positive action is unclear. Last but not least, further studies on the safety of MT are still needed. This article reviews the role of MT in I/RI treatment and related mechanisms over the past 10 years.