The long‐lasting activity of photosensitizers during photodynamic therapy (PDT) causes excessive damage and arouses great concerns about biosafety. Herein, we synthesized a pyridinium‐decorated diiodo‐BODIPY compound (PyBDP) and investigated its photosensitizing activity under hypoxic condition in the presence of NADH that is abundant in the mitochondria of hypoxic tumors. The unique property of PyBDP lies in the redox environment‐dependent photo‐response. At green light exposure, PyBDP is converted into a colorless inactive form by interacting with NADH in a two‐step one‐electron transfer process. Interestingly, the NADH‐dependent hydrogenation of PyBDP is affected by the presence of cytochrome c (Cyt cox) that is an important component of mitochondrial electron transport chain (Mito‐ETC), unless Cyt cox is exhausted. Active radical species is produced during the photocatalytic reaction, which adds the understanding of PyBDP‐induced photodamage. Therefore, we applied the strategy of auto‐deactivation PDT using a BODIPY photosensitizer by tethering triphenylphosphonium to PyBDP. After PDT effect in a type I pathway, the photosensitizer underwent almost entire auto‐deactivation in hypoxic HeLa cells. This work paves a way for the development of reductive PDT with enhanced safety and efficacy in fighting hypoxic tumors independent on reactive oxygen species (ROS).