Mitophagy, the process in which cells degrade dysfunctional organelles and recycle their nutrient substances by lysosomes, plays a vital role in cell metabolism and physiology. Herein, we present a highly targeting and near-infrared (NIR) mitochondrion fluorescent probe, which can monitor the process of autophagy. The response mechanism of the probe is based on intramolecular charge transfer (ICT) for the detection of autophagy and real-time imaging of living cells. We designed a primary amine as a pH sensitizing group, and due to the ICT process, the probe exhibits green fluorescence, and when it is protonated the ICT process is broken, and the NIR fluorescence will be restored. Simultaneously, the green fluorescence of the probe disappears. This probe exhibits excellent selectivity, high sensitivity and clean responsiveness, which indicate that it can be applied for high-targeting and high-sensitive imaging of the process of autophagy in living systems.