SO2 is recognized as the fourth gas messenger followed by NO, H2S and CO, it plays pivotal roles in many cellular activities and apoptosis in mitochondria and lysosomes. However, current molecular tools for of sensing SO2 in mitochondria and lysosomes respectively, which is not conducive to well defining the functions and relationships between mitochondria- and lysosome-SO2 in regulation of cellular activities. Thus, it is critical to develop powerful tool to detect mitochondria- and lysosome-SO2 simultaneously. Herein, we have rationally designed and synthesized a novel fluorescent probe DML-P based on a dual organelle-targeted groups for imaging SO2 in mitochondria and lysosomes simultaneously for the first time. The novel probe showed well water-solubility, high selectivity and high stability. Furthermore, probe has achieved in tracing endogenous SO2 with two stimulation methods by one- and two-photon modes. Significantly, the probe has succeeded in tracing endogenous SO2 in lysosomes and mitochondria concurrently in living cells. We hope this probe could provide a significative tool for studying the system functions and connections of mitochondria-and lysosomes-SO2.