Developing single fluorescent probe for simultaneously visualizing mitophagy flux and oxidative stress with super-resolution is highly demanded yet quite challenging. Herein, we design and synthesize a ratiometric HClO probe AHOH, which is capable of simultaneously staining lysosomes and mitochondria with red and green color, respectively. AHOH could be selectivity oxidized by HClO, leading to a large emission blue shift (90 nm) and an over 1300-fold enhancement of the emission ratio of Fl547 nm/Fl637 nm. We apply AHOH in super-resolution microscopy and clearly visualize the dynamics of mitochondria-lysosomes interactions and the oxidative stress states upon different stimuli. Mitochondria dysfunction triggered by different drugs and genetic defect lead to elevated oxidative stress and higher levels of mitophagy. Moreover, AHOH could serve as a reliable tool for evaluating the efficacy of drugs regulating mitochondria dysfunction. This work provides a powerful dual-color super-resolution imaging agent for real time monitoring the dynamics of organelle interactions and oxidative stress.