Photofrin-mediated photodynamic therapy (PF-PDT) can induce cell apoptosis via the mitochondria/caspase-3 pathway. Here, we further investigate the mechanism involved in the mitochondrial apoptotic process induced by PF-PDT. A high-level intracellular reactive oxygen species (ROS) generation in mitochondria, mitochondrial swelling, and dissipation of mitochondrial transmembrane potential were observed immediately after irradiation, indicating that mitochondria were the major ROS generation sites and also the first oxidative damage sites after PF-PDT treatment. For mitochondrial permeability detection, the decrease of calcein fluorescence emission intensity and release of cytochrome c were observed immediately after PF-PDT treatment, indicating the occurrence of mitochondrial inner membrane permeabilization (MIMP) and the mitochondrial outer membrane permeabilization (MOMP). However, cytochrome c release was not prevented by cyclosporine (CsA), a specific inhibitor of mitochondrial permeability transition (MPT). Taken together, these results demonstrated that PF-PDT caused simultaneous onset of MIMP and MOMP immediately after the treatment, and MOMP was independent of the MPT. Besides, inducible mitochondrial ROS generation played key roles in PF-PDT-induced cell apoptosis. This study will be benefit for understanding the mechanism involved in the initial mitochondrial oxidative damage by PF-PDT.