Boron-dipyrromethene (BODIPY) as a traditional fluorescent dye has received increasing attention because of its high molar extinction coefficient, easy modification, and good light stability. In this work, three BODIPY compounds (BDP-1, BDP-2 and BDP-3) were designed and synthesized by introducing PEG chains and a naphthalimide (NI) group onto the parent structure of BODIPY. Due to the electron-withdrawing properties of NI, the compounds of BDP-2 and BDP-3 formed a typical donor (D)-acceptor (A) structure, which led to the red-shifted absorption and fluorescence spectrum. The synthesized BODIPY exhibited intense green emission, with fluorescence quantum yield of 0.66, 0.29, and 0.19 for BDP-1, BDP-2 and BDP-3 respectively. The decrease in fluorescence of BDP-2 and BDP-3 was probably ascribed to the enhanced intramolecular charge transfer because of the introduction of the NI group. The good biocompatibility and low cytotoxicity of the synthesized BODIPY compounds were verified by the CCK-8 assay. The subcellular localization of the three compounds was further evaluated through a confocal laser scanning microscope. The results showed that these BODIPY derivatives were mainly localized in the lysosomes of cancer cells. Thus, the synthesized BODIPY fluorescent dyes show promising applications in tumor imaging benefiting from their good biocompatibility and strong fluorescence.