Microbial infection often accompanies most diseases such as cancer, which has been testified to severely decrease the efficacy of cancer therapy. It is imperative and significant to develop the single therapeutic agents with high antimicrobial and antitumor efficacy. Herein, fluoroalkylated boron dipyrromethene (BDP) (named as B-F) and its counterpart alkylated BDP (named as B-H) were synthesized. Fluoroalkylation could facilitate the spontaneous self-assembly of B-F into nanoparticles (NPs) and dramatically enhance its intracellular delivery efficiency. Furthermore, compared with B-H NPs, B-F NPs possessed enhanced capacity of generating reactive oxygen species (ROS) upon irradiation, which endowed B-F NPs with photodynamic destroying Gram-positive bacteria and cancer cells. This work contributes to strategical design of the nanoscale photosensitizers (PSs) for antimicrobial photoinactivation and photodynamic therapy (PDT). Display omitted