Enhancing the interactions between photosensitizers and bacteria is key to developing effective photodynamic antibacterial agents. However, the influence of different structures on the therapeutic effects has not been systematically investigated. Herein, 4 BODIPYs with distinct functional groups, including the phenylboronic acid (PBA) group and pyridine (Py) cations, were designed to explore their photodynamic antibacterial activities. The BODIPY with the PBA group (IBDPPe-PBA) exhibits potent activity against planktonic Staphylococcus aureus (S. aureus) upon illumination, while the BODIPY with Py cations (IBDPPy-Ph) or both the PBA group and Py cations (IBDPPy-PBA) can significantly minimize the growth of both S. aureus and Escherichia coli (E. coli). In particular, IBDPPy-Ph can not only eliminate the mature S. aureus biofilm and E. coli biofilm in vitro, but also promote the healing of the infected wound. Our work provides an alternative for reasonable design of photodynamic antibacterial materials.