Mitochondria-targeted pH probes often face challenges in p K a alignment with the mitochondrial matrix (pH~8.0), limiting their utility for dynamic pH monitoring. In this paper, three mitochondria−targeted near−infrared fluorescent probes 5a−5c were developed by introducing nitrogen atom at the 4−position of Nile Blue and modulating p K a through the formation of intramolecular hydrogen bonding. Probes 5a−5c exhibited ultra−high molar extinction coefficients up to 10 5 M −1 cm −1, along with excellent photostability and sensitive pH response. The fluorescence intensities of 5a−5c enhanced 12~14−fold, while the fluorescence quantum yields increased from 1.2%−2.5% to 13%−16% with the pH decreasing from 10 to 4.0 (only 0.5% cosolvent). In addition, terrific linear relationships between pH and fluorescence intensity were established with high correlation coefficient (R 2 = 0.99) from pH 5.2 to 9.2. Based on the exceptional low toxicity and mitochondrial targeting ability, 5a−5c migrated from mitochondria to lysosomes during starvation and rapamycin−induced autophagy, allowing real−time tracking of mitochondrial pH variations using fluorescence intensity and colocalization coefficient as parameters. Notably, dynamic changes between mitochondria and lysosomes were real-time observed in the mitochondrial damage model constructed by hydrogen peroxide. In conclusion, probes 5a−5c have excellent optical properties and biocompatibility, underscoring their significance in monitoring mitochondrial physiological and pathological processes.