The development of photosensitizer for cancer photodynamic therapy has been challenged due to its low photostability and therapeutic inefficacy under hypoxic tumor microenvironment. To overcome the issues, we developed a mitochondria targeting photosensitizer consisting of indocyanine moiety with a triphenylphosphonium arms, which can self-assemble into spherical micelles and direct to mitochondria. Self-assembling of the photosensitizer exhibited a higher photostability by preventing free rotation of the indoline ring of the indocyanine moiety. The mitochondria targeting capability of the photosensitizer conferred them to utilize intramitochondrial oxygen content. We found that the mitochondria targeting photosensitizer localized into mitochondria and induced apoptosis of cancer cells even under hypoxia condition through generation of mitochondrial ROS. The micellar self-assembles of the photosensitizer was further confirmed to localize into tumor tissue in xenograft tumor mice model through the passive targeting and showed efficient tumor growth inhibition.