The invention discloses a mitochondrion-targeted fluorinion fluorescence probe, and a preparation method and applications thereof, and belongs to the technical field of analytical chemistry. The structure of the mitochondrion-targeted fluorinion fluorescence probe is represented by a formula in the invention. Synthesis of the mitochondrion-targeted fluorinion fluorescence probe is realized via three steps; the post-treatment process is relatively simple; fluorinion probe rapid selective detection is realized; selectivity is high; the capacity in resisting influences of other molecules is high; the mitochondrion-targeted fluorinion fluorescence probe can be used for detection of fluorinion in cells; compared with commercial available mitochondrion dye, the mitochondrion-targeted fluorinion fluorescence probe possesses following advantages: the superposition rate on fluorinion imaging in mitochondria is high, the co-location coefficient of the two dyes is 0.89, and it is confirmed that the mitochondrion-targeted fluorinion fluorescence probe can be taken as an intracellular mitochondrion fluorinion detection probe.