The changes in viscosity and the concentration of ONOO- in mitochondria can effectively reflect the physiological and pathological status of cells. Therefore, the development of effective fluorescent probes for the sensing of viscosity and the concentration of ONOO- in mitochondria has great significance. In this article, a mitochondrial targeted fluorescent probe named Mito-RP was synthesized for the dual responsive sensing of viscosity and ONOO- by introducing pyridine ring and phenylboronic acid ester structure into 4-dimethylamino-cinnamaldehyde with long conjugated chain structure as the parent material. Mito-RP exhibits 600 folds fluorescence enhancement of viscosity in the red-light channel at 700 nm, with pyridine cation as the mitochondrial anchoring group. Simultaneously, Mito-RP appears excellent selectivity towards ONOO- using boronic acid esters as response sites. A new ratio fluorescence analysis method was constructed based on the linear correlation between the emission intensity ratio of Mito-RP at 616 nm/700 nm and the concentration of ONOO-. The linear range is 0.05-33 μM and the detection limit is 9.2 nM. Meanwhile, Mito-RP successfully monitored the changes in viscosity during lipopolysaccharide induced inflammation and rapamycin induced mitochondrial autophagy in HeLa cells. In addition, Mito-RP has also achieved visual imaging of intracellular exogenous/endogenous ONOO-. These studies provide a novel method for in-depth investigation of mitochondrial function and its role in diseases.