Nanomaterials (NMs) have extensive application potential in drug delivery, tissue engineering, and various other domains, attributable to their exceptional physical and chemical properties. Nevertheless, an increasing body of literature underscores the diverse safety risks are associated with NMs upon interaction with the human body, including oxidative stress and programmed cell death. Mitochondria, serving as cellular energy factories, play a pivotal role in energy metabolism and the regulation of cell fate. Organs with substantial energy demands, including the heart and brain, are highly sensitive to mitochondrial integrity, with mitochondrial impairment potentially resulting in significant dysfunction and pathologies such as as heart failure and neurodegenerative disease. This review elucidates the pathways by which NMs translocate into mitochondria, their intracellular dynamics, and their impact on mitochondrial morphology, respiratory chain activity, and metabolic processes. We further investigate associated molecular mechanisms, including mitochondrial dynamic imbalance, calcium overload, and oxidative stress, and elucidate the pivotal roles of mitochondria in different forms of programmed cell death such as apoptosis and autophagy. Finally, we offer recommendations regarding the safety and efficacy of NMs for medical applications. By systematically analyzing the interactions and molecular mechanisms between NMs and mitochondria, this paper aims to enhance the toxicological evaluation framework of NMs and provide a foundational reference and theoretical basis for their clinical utilization.