As a non-invasive cancer therapy method, photodynamic therapy (PDT) shows tremendous promise in clinical cancer treatment. Light-activated singlet oxygen production of photosensitizers (PSs) is the prerequisite for cancer PDT, and the use of organic photosensitizers is always limited by visible light-based activation, hydrophilicity, biocompatibility, selectivity and quantum yield of singlet oxygen. Currently, both zinc porphyrin- and BODIPY-based structures have been widely used in the development of PDT PSs. Here, we developed a novel naphthalimide bridged zinc porphyrin/BODIPY molecule (Por-BDP-1) with two poly(ethylene glycol) (PEG) chains, in which D-A structure was constructed between the naphthalimide group and porphyrin group. After self-assembly into nanoparticles, Por-BDP-1 NPs (Diameter: 122.4 nm) could quench fluorescence in 600–700 nm, bind with calf thymus-DNA, and produce singlet oxygen during light-irradiation (laser: 680 nm, 1.0 W/cm[Formula: see text]. In addition, Por-BDP-1 NPs effectively killed HeLa cells with a IC[Formula: see text] value = 44.8 μg/mL and showed a lower dark toxicity under the same conditions. All our results demonstrated that our naphthalimide bridged zinc porphyrin/BODIPY nano-photosensitizer is a promising nanoagent for PDT in the clinic.