Tracking of mitochondrial dynamic processes including their morphology, biogenesis and elimination is of significance to deeply understand mitochondrial physiology and related diseases, which requires simultaneous and discriminative labeling of both mitochondria themselves and correlated downstream organelles. However, the combination of multiple fluorescent probes will bring the large invasive effect that seriously impacts the normal physiological processes of mitochondria within live cells. To address this issue, we herein construct a single molecular probe through the combination of two pH-sensitive fluorogens, hydroxyl-coumarin and rhodamine B, enabling the detection of intracellular microenvironmental pH variations. Importantly, the as-synthesized probe not only accumulates into mitochondria, indicated by cyan emission from hydroxyl-coumarin but also can be delivered to the downstream acidic autolysosomes upon the occurrence of mitophagy, indicated by red emission from rhodamine B. Taking advantage of a two-channel confocal microscopy strategy, we have achieved to real-time track the processes of mitochondrial replication, merge and autophagy.