Antibacterial photodynamic therapy (APDT), which is a non-invasive treatment method, is based on the interaction between near-infrared light and a nontoxic photosensitizer concentrated at the lesion site to generate reactive oxygen species (ROS). These species are highly cytotoxic in virtually all bacteria. With the development of biomaterials and nanotechnology, advances in nano-biotechnology have resulted in the optimization of biocompatibility and biosafety of small-molecule photosensitizers. The targeting ability has improved and the quantum yield under illumination has significantly increased. Nanotechnology exhibits excellent clinical application prospects with respect to antimicrobial therapy. In this review, recent applications and developments of APDT are summarized by combining various modification strategies and mechanisms for nanophotosensitizers.