Mitochondria are essential for maintaining cellular survival and function, and their dysfunction is implicated in cancer, cardiovascular abnormalities, neurodegenerative diseases, aging, and so on, carrying significant pathophysiological implications. Conducting research focused on mitochondria helps elucidate the mechanisms of disease development and offers new therapeutic perspectives for combating challenging conditions like malignant tumors, myocardial injury, Parkinson's disease, and other related ailment. In recent years, the flourishing development of near-infrared (NIR) technology has provided powerful tools for mitochondrial research. NIR light serves as both an information carrier for biological imaging and analysis, and as a non-invasive stimulus in drug delivery, phototherapy, and energy conversion applications. Currently, a large number of NIR materials have been applied to target mitochondria in disease diagnosis, treatment, and theranostics. These materials have garnered significant attention due to their unique properties and remarkable in vivo performance. This review aims to provide researchers developing mitochondria-targeted NIR materials for biomedical applications with an advanced and comprehensive guide. It not only offers valuable insights into design strategies, material properties, and applications in disease diagnosis and treatment, such as strategies to improve imaging sensitivity, specificity, and therapeutic efficacy, but also delves into the existing challenges in the field, issues that persist in clinical translation, and future prospects.