ABSTRACT Mitochondria, known as the energy powerhouses of cells, also have a significant role in the innate immune response. Consequently, maintaining mitochondrial homeostasis is crucial for overall organismal health. Mitochondrial quality is tightly regulated through processes such as mitochondrial dynamics and mitophagy. However, compared to mammals, the regulatory roles of mitochondria and mitophagy in fish immunity have been less extensively studied. This article provides a comprehensive review of mitochondrial quality control and mitophagy mechanisms, with a particular focus on summarizing the mitochondrial antiviral signaling (MAVS) pathway and its interactions with viruses in fish. Additionally, it explores the interplay between MAVS and innate immunity, the association between mitophagy and viral infections in fish, and how the regulation of mitophagy can promote fish health. By enhancing the understanding of the functions of mitochondria and mitophagy in fish immunity, this review offers valuable insights for disease prevention, control, and the sustainable development of fish populations.