Photodynamic antibacterial therapy shows great potential in bacterial infection and the reactive oxygen species (ROS) production of the photosensitizers is crucial for the therapeutic effect. Introducing heavy atoms is a common strategy to enhance photodynamic performance, while dark toxicity can be induced to impede further clinical application. Herein, a novel halogen-free photosensitizer Aza-BODIPY-BODIPY dyad NDB with an orthogonal molecular configuration was synthesized for photodynamic antibacterial therapy. The absorption and emission peaks of NDB photosensitizer in toluene were observed at 703 nm and 744 nm, respectively. The fluorescence (FL) lifetime was measured to be 2.8 ns in toluene. Under 730 nm laser illumination, the ROS generation capability of NDB was 3-fold higher than that of the commercial ICG. After nanoprecipitation, NDB NPs presented the advantages of high photothermal conversion efficiency (39.1%), good photostability, and excellent biocompatibility. More importantly, in vitro antibacterial assay confirmed that the ROS and the heat generated by NDB NPs could extirpate methicillin-resistant S. aureus effectively upon exposure to 730 nm laser, suggesting the potential application of NDB NPs in photo-initiated antibacterial therapy.