Mitochondria are essential organelles in eukaryotic cells and act as the energy powerhouse and biosynthetic compartment. Fluorescent dyes are widely used powerful molecular tools for analytical sensing and optical imaging. Low photostability, short excitation and emission wavelengths, and aggregation-induced quenching effects restrict the application of traditional commercial mitochondrial fluorescent probes for bioimaging. In this study, using rhodamine as the acceptor and phenothiazine as the donor, we synthesized a novel mitochondrial-targeted near infrared (NIR) fluorescent probe, MIT-PZR. Due to low cytotoxicity, great photostability and high specificity for mitochondria targeting, MIT-PZR has enormous potential for cell imaging. Furthermore, with a sizeable Stokes shift (emission peak at 705 nm), MIT-PZR penetrated tissues providing stable red fluorescence for imaging in vivo. The histological assessment of various tissues after treatment with MIT-PZR indicated that it has good biocompatibility. Thus, MIT-PZR is a promising mitochondrial NIR fluorescent probe for future application in clinical diagnosis and modern biological research.