Near-infrared (NIR) photodynamic therapy (PDT) is a promising antitumor strategy under NIR light irradiation to kill cancer cells. Mitochondria has a critical function in sustaining cellular viability and death, which is the ideal organelle for PDT. Here, we reported a tetraphenylporphine (TPP)-conjugated amphiphilic copolymer and an iodinated boron dipyrromethene photosensitizer (BDPI) with high singlet oxygen yield to form nanoparticles (PBDPI-TPP), which could realize mitochondria-targeting and improve the NIR imaging-guided PDT. The as-prepared mitochondria-targeting nanoplatform could show effective subcellular localization and bring about significant irreversible mitochondrial injury for enhanced PDT. Both in vitro and in vivo experiments revealed that the mitochondria-targeting PDT system could achieve a remarkable therapeutic effect, indicating that it is a promising nanoplatform for NIR imaging-guided PDT in cancer therapeutics.