Hydrogen peroxide (H2O2), as important products of oxygen metabolism, plays an important role in many biological processes, such as immune responses and cellular signal transduction. However, abnormal production of H2O2 can damage cellular biomolecules, which was closely associated with many diseases. Thus, it is urgent to monitor the level change of H2O2 in living cells, particularly at subcellular levels. Toward this end, a wide variety of H2O2 fluorescent probes have been designed, developed and applied for imaging of H2O2 in subcellular levels. In this review, we highlight the representative cases of H2O2 fluorescent probes with mitochondria, nuclei and lysosomes-targetable ability. The review contains organelle target strategies, structures, fluorescence behavior and biological applications of these probes.