Mitochondria are widely known as the energy factories of eukaryotic cells and have multiple important functions in different cellular processes. Dysfunction within mitochondria is a catalyst for various diseases, leading to widespread cell death. An increasing number of studies on repairing damaged mitochondria indicate that mitochondria are important targets for disease treatment interventions. However, the limited clinical practice and low cure rate mean that the limitations of traditional drugs need to be further overcome. Nanotechnology has achieved good region specific biological distribution and high efficacy by utilizing excellent nanomaterials and targeted drug delivery. Mitochondrial repair nanomedicine has achieved ideal therapeutic effects. This review elucidates the importance of mitochondria in various cells and organs, and also compiles mortality data for related diseases. Correspondingly, the therapeutic strategies mediated by nanomedicine and the mitochondrial repair nanomedicine applicable to diseases were introduced in detail, fully understanding the role of mitochondrial dysfunction and the advantages of nanomedicine. In addition, there was extensive discussion on future challenges and directions. In summary, this review provides comprehensive insights into the design and development of mitochondrial repair nanomedicines, aimed at assisting scientists who wish to expand their research fields and engage in this interdisciplinary topic.