Sensitive and selective detection and imaging of nitroreductase (NTR) in cancer cells is of great importance for better understanding their biological functions. Since there are a few fluorescent probes concerning NTR activity specifically located in mitochondria, we developed a novel fluorescent benzoindocyanine probe (BICP) for mitochondrial NTR activity monitoring and imaging via extending a benzoindole moiety into a benzoindocyanine based fluorophore (BICF) with a strong intramolecular charge transfer (ICT) effect and incorporating 4-nitrobenzyl as a fluorescence-quenching and enzyme-responsive moiety. Live cell imaging of HeLa and A549 demonstrates that the developed BICP is able to realize sensitive and selective mitochondrial NTR activity probing with high-contrast "off-on" fluorescence. These findings implied the great potential of the developed probe for monitoring mitochondrial-specific NTR activities in living cells and related applications in cell biology.