Thiobases or sulfur-substituted nucleobases have been developed and recognized as prospective class of heavy-atom-free photosensitizer for photodynamic therapy due to their appealing phototherapeutic properties. In this work, we have prepared the thionated BODIPY analogues by replacing oxygen with sulfur atom at exocyclic carbonyl group, which display red-shifted absorption band, remarkable fluorescence quenching and high singlet oxygen quantum yield as well as excellent photostability. Sulfur substitution stabilizes the LUMO level and destabilized the HOMO, and thus reduces the energy gap and shift the absorption to long wavelength. The replacement of O by S-atom is essential for the enhancement of the intersystem crossing from the singlet excited state to the reactive triplet state. DFT calculations revealed that large spin-orbit coupling (SOC) could be responsible for the efficient population of the triplet state. In addition, the thionated BODIPY efficiently generates the intracellular reactive oxygen species (ROS) with low cytotoxicity. These studies demonstrate that the thionated BODIPY analogue is potentially suitable for use as a photosensitizer.