Thio-caged fluorophores can be effectively desulfurized into their oxygenated derivatives through visible light, thereby restoring the strong emission, and are applied inlive cell super-resolution imaging. Herein, we theoretically investigated the reasons for the low fluorescence quantum yields of a series of thio-caged fluorophores and the underlying reasons for the differences in fluorescence quantum yields of their oxygenated derivatives. The calculation results show that the S atom on the thiocarbonyl group is more likely to excite n electrons to form the nÏ* state, which reduces the energy of the nÏ* state and leads to fluorescence quenching. In contrast, oxygenated derivatives is more likely to excite Ï electrons to form ÏÏ* state, which is the main reason for restoring the strong emission of fluorophore. Meanwhile, the calculation results show that the difference of fluorescence intensity caused by oxygenated derivatives is determined by the number of the carbonyl group, which affects the vibronic coupling between ÏÏ* and nÏ* states and thereby leads to fluorescence quenching. These results can effectively reveal the fluorescence quenching mechanism of thio-caged fluorophores and the luminescence mechanism of their oxygenated derivatives, and provide correct and guiding design strategies for the development of new thio-caged fluorophores.