The mitophagy assay is an experimental method used to assess the levels of mitophagy in cells. Technologies such as fluorescent probes, protein markers, or electron microscopy are usually used to monitor the fusion of autophagic vacuoles and mitochondria in cells. Mitophagy, also known as the progressive degradation of mitochondria, is an important process for maintaining mitochondrial quality and function within cells. This research helps understand the role of mitophagy in cell survival, stress response, and a variety of diseases, such as neurodegenerative diseases and tumors.