Biothiols are implicated in different physiological and pathological processes, while abnormal levels of biothiols are related to numerous diseases. It is essential to discriminatively detect these molecules and explore their inherent transformation in living biological samples. Herein, dual-reactive and dual-quenching fluorescent probes based on thiolysis of NBD (7-nitro-1,2,3-benzoxadiazole) thioether/ether/amine for separate detection of H2S and Cys/Hcy were rationally designed. Probe 2 was able to sense H2S (λex/em = 405/455 nm) and Cys/Hcy (λex/em = 470/550 nm) in the presence of GSH in aqueous buffer. Moreover, the probe not only could be applied for visualization of exogenous H2S and Cys in living cells but also successfully showcased the potential to verify the biosynthesis of endogenous H2S from Cys.