Mitochondria-targeted cancer therapies have proven to be more effective than other similar non-targeting techniques, especially in photodynamic therapy (PDT). Indocyanine dye derivatives, particularly IR-780, are widely known for their PDT utility. However, poor water solubility, dark toxicity, and photobleaching are limiting factors for these dyes, which otherwise show promise based on their good absorption in the near-infrared (NIR) region and mitochondria targeting ability. Herein, we introduce an indocyanine derivative (IR-Pyr) that is highly water soluble, exhibiting higher mitochondrial targetability and better photostability than IR-780. Furthermore, electrostatic interactions between the positively charged IR-Pyr and negatively charged hyaluronic acid (HA) were utilized to construct a micellar aggregate that is selective towards cancer cells. The cancer mitochondria-targeted strategy confirms high PDT efficacy as proved by in vitro and in vivo experiments.