Mitochondria are the energy factory of cells and can be easily damaged by reactive oxygen species (ROS) because of the frequent occurrence of oxidative stress. Abnormality in mitophagy is often associated with many diseases including inflammation, cancer, and aging. While previously developed fluorescent probes mainly focus on detecting just ROS or mitophagy, quite rare studies have endeavored to comprehensively capture the entire mitophagic process, encompassing both the production of ROS and the induction of mitophagy. Herein, we report a new ratiometric fluorescent probe NA-DP for tracking peroxynitrite (ONOO-) as well as the subsequent oxidative stress-induced mitophagy. To a naphthalimide-based dye, an ONOO--responsive diphenyl phosphinate moiety and the mitochondria-targeting triphenylphosphonium group were attached. The probe showed a highly selective response to ONOO- through an addition-elimination reaction with diphenyl phosphinate. Owing to its outstanding pH stability and organelle-targeting ability, NA-DP was successfully used to detect mitophagy induced by oxidative stress after the generation of ONOO-. In the meantime, the probe was also used to track starvation-induced mitophagy and indicate that starvation-induced mitophagy is independent of ONOO-. Therefore, NA-DP has the ability to precisely track oxidative stress-induced mitophagy by distinguishing it from starvation-induced mitophagy. This study offers a new chemical tool to study the relationship between ROS generation and mitophagy.