Hydrogen sulfide (H2S) in mitochondria plays important roles in many mitochondria-related physiological and pathological processes. Herein, a cyanine/naphthalimide hybrid fluorescent probe, L1, was designed for the ratiometric detection and imaging of mitochondrial H2S, in which cyanine and naphthalimide were used as the mitochondria-targeting group and H2S response group, respectively. Besides its good mitochondria-targeting ability, L1 also showed high sensitivity and good selectivity for H2S. Moreover, on the basis of the fluorescence ratio of naphthalimide to cyanine fluorophore, it was successfully applied to monitor the endogenous and exogenous mitochondrial H2S in live cells. Additionally, the endogenous mitochondrial H2S in different cell lines was measured by probe L1.