Irregularities in mitochondrial viscosity and peroxynitrite (ONOO-) concentration can lead to mitochondrial dysfunction. It is still a great challenge to develop near-infrared (NIR) fluorescent probes to simultaneously detect viscosity, endogenous ONOO-, and mitophagy. Herein, a multifunctional mitochondria-targeting NIR fluorescent probe P-1 was first synthesized for simultaneously detecting viscosity, ONOO-, and mitophagy. P-1 used quinoline cations as a mitochondrial targeting moiety, arylboronate as an ONOO- responsive group, and detected the change of viscosity by the twisted internal charge transfer (TICT) mechanism. The probe has an excellent response to the viscosity during inflammation by lipopolysaccharides (LPSs) and mitophagy induced by starvation at 670 nm. The viscosity changes of the probe induced by nystatin in zebrafish showed that P-1 was able to detect microviscosity in vivo. P-1 also showed good sensitivity with a detection limit of 6.2 nM for ONOO- detection and was successfully applied to the endogenous ONOO- detection in zebrafish. Moreover, P-1 has the ability to distinguish between cancer cells and normal cells. All of these features make P-1 a promising candidate to detect mitophagy and ONOO- -associated physiological and pathological processes.