Mitochondrial autophagy, known as mitophagy, is a vital cellular process that involves the selective degradation of damaged or dysfunctional mitochondria through autophagy, which is critical to the functional integrity of the entire mitochondrial network and determines the survival and death of cells. An abnormal pH may lead to an imbalance in mitochondrial homeostasis and the occurrence of mitochondrial autophagic acidification and dysfunction. SCN- is also an important anion in cellular metabolism, and its abnormal concentration may lead to mitochondrial damage. However, so far, there are few reports on the simultaneous realization of pH and SCN- detection in mitochondria. Therefore, to complement the blank in this area, we developed the polysiloxane-based fluorescent probe P0-CMN that is capable of simultaneously visualizing pH and SCN- fluctuation levels in mitochondria. The probe P0-CMN has the desired mitochondrial-targeting properties and sensitivity to pH and SCN-. It is able to simultaneously monitor pH and SCN- changes in mitochondria in a dual-channel mode. In addition, probe P0-CMN can visualize pH changes during mitochondrial autophagy. This work provides an effective strategy for the design of dual-responsive fluorescent probes and further broadens the application of polysiloxane fluorescent materials.