Photodynamic therapy (PDT) has garnered significant interest as a promising approach for cancer treatment due to its effectiveness, versatility, and non-invasiveness. However, its clinical application is hindered by several factors, such as suboptimal efficacy, poor targeting capabilities, shallow penetration depth, and safety concerns. Herein, we introduce B-SQ, a novel nano-photosensitizer that addresses these challenges. B-SQ is a self-assembling, cancer mitochondria-targeting agent that is both activatable and photodegradable, designed by strategically modifying a near-infrared fluorescent squaraine dye. We extensively assessed the PDT potential of B-SQ in various cancer cell models and explored the molecular mechanisms of PDT-induced cell death. Importantly, B-SQ demonstrated high specificity for cancer cells, and its PDT efficiency was activatable, with near-infrared fluorescence to distinguish cancer cells from normal cells. This work provides the first evidence of B-SQ inducing the intrinsic mitochondrial apoptosis pathway and cell cycle arresting in cancer cells via PDT. Additionally, its photodegradable nature is likely to minimize side effects after treatment. This research introduces an innovative class of nano-photosensitizers that are activatable, targeting cancer mitochondria, and are photodegradable with near-infrared fluorescence. These qualities present new possibilities for safer and more effective clinical cancer treatments in the future.