The invention discloses a water soluble mitochondrial targeting imaging probe and a preparation method thereof. The structural formula of compounds that form the water soluble mitochondrial targeting imaging probe can be formula (I), (II), (III), (IV), (V), or (VI). The water soluble mitochondrial targeting imaging probe has the characteristics of good water solubility, high resistance to photo-bleaching, high thermal stability, low toxicity, and high sensitivity. Hela, MCF-7, and NIH-3T3 cells are taken as the models to observe the distribution situation of the fluorescent probe in cells through a laser con-focal microscopy technology; the results show that the probe is mainly distributed in mitochondrial, and the targeting property is good. The test results show that the provided probe has the characteristic of strong mitochondrial targeting imaging performance on cancer cells and non-cancer cells; thus an effective means is provided for quantitatively research superoxide radicals in cells in time and space, and thus the pathologic and physiological mechanisms of active oxygen radicals can be researched.