Herein, by optimizing phenyl selenide-based BODIPYs, BDP-Se-MOS was obtained, which possessed resistance to ROS and could selectively detect Cys. BDP-Se-MOS could not only discriminate between normal and cancer cells, but also image Cys levels in tumor-bearing mice in real time as well as image the fluctuations of Cys levels in an APAP-induced DILI model.