A novel near-infrared fluorescent probe for detection of bisulfite was designed and developed based on a conjugated naphthopyran-indolium system. The sensor showed excellent selectivity, high sensitivity and a rapid response toward bisulfite in aqueous solution. Upon the addition of HSO3−, the sensor displayed 21.6-fold (I520/I653) fluorescence intensity enhancement, accompanied with an apparent color change from violet to colorless, suggesting that the sensor can be used to detect HSO3− with “naked-eye”. The lowest detection limit for the above measurement was found to be 76 nM, and it was sensitive enough for the detection of endogenously produced bisulfite in biological system. Furthermore, the sensing mechanism was confirmed by high-resolution mass spectroscopy analysis and 1H NMR spectrometry analysis, which was based on the strong nucleophilic addition reaction of bisulfite towards the sensor. Moreover, as a biocompatible molecule, the probe was successfully used for fluorescence imaging of bisulfite in MCF-7 cells and zebrafish, demonstrating that the probe is a novel ratiometric fluorescent probe to image SO2 derivatives in biosystem.