The past decades have witnessed great strides in phototherapy as an experimental option or regulation-approved treatment in numerous cancer indications. Of particular interest is nanoscale photosensitizer-based phototherapy, which has been established as a prominent candidate for advanced tumor treatment by virtue of its high efficacy and safety. Despite considerable research progress on materials, methods and devices in nanoscale photosensitizing agent-based phototherapy, their mechanisms of action are not always clear, which impedes their practical application in cancer treatment. Hence, from a new perspective, this review elaborates the working mechanisms, involving impairment and moderation effects, of diverse phototherapies on cells, organelles, organs, and tissues. Furthermore, the most current available phototherapy modalities are categorized as photodynamic, photothermal, photo-immune, photo-gas, and radio therapies in this review. A comprehensive understanding of the inferiority and superiority of various phototherapies will facilitate the advent of a new era of cancer phototherapy.