Hypochlorite (ClO−), one of reactive oxygen species (ROS), is closely related with many physiological and pathological processes. Especially as one of cellular reactive oxygen species in mitochondria, ClO− can induce mitochondrial permeability, which leads to apoptosis. Thus, developing an effective method which is able to sense ClO− in mitochondria is important. Although fluorescent probe has become a powerful tool for imaging ClO− in mitochondria, most of them suffered from phototoxicity to biosamples, autofluorescence, and photobleaching phenomenon due to their short-wavelength excitations and emissions. Based on advantages of two-photon fluorescent probe and far-red to NIR fluorescent probe, a mitochondria-targetable two-photon fluorescent probe with a turn-on signal in far-red to NIR region, Mito-TP-ClO, was developed for ClO− in this paper. Mito-TP-ClO is consisted of a triphenylphosphonium cations as a mitochondria-targetable unit and a structure of dibenzoylhydrazine as a response unit to ClO−. Mito-TP-ClO exhibited a high sensitivity and a high selectivity to ClO−, with a linear range from 6.0 × 10−8 to 1.0 × 10−5 M and a detection limit of 2.5 × 10−8 M. Due to its large two-photon cross section (267 GM) and far-red to NIR emission, Mito-TP-ClO exhibits excellent performances including low autofluorescence, photostable fluorescence signal, and deep tissue penetration (230 μM). Moreover, Mito-TP-ClO was successfully used to detect endogenous ClO− in bacteria-infected cells and inflammatory mouse model, which confirmed that Mito-TP-ClO is a powerful tool to monitor ClO− in mitochondria and study on effects of hypochlorite on mitochondria.