Zeolite imidazolate frameworks (ZIFs) have been widely used in drug delivery and antibacterial applications due to their highly controllable structure and pore size. However, the relationship between the structure of ZIFs and their antibacterial efficacy has not been fully elucidated. In this study, three ZIFs with uniform sizes and specific morphologies were synthesized: cubic (Z-8), leaf-like (Z-L), and flower-like (FZ-L). Flow cytometry was employed to assess the effects of these materials on Bacillus subtilis and Escherichia coli at different concentrations and exposure times. Results showed that sharp-edged ZIFs possess enhanced antibacterial effects. Specifically, FZ-L exhibited the lowest minimum inhibitory concentration of 400 μg/mL and a minimum bactericidal concentration of 20 μg/mL, which can kill bacteria effectively and rapidly. Further study on the antibacterial mechanisms showed that these materials do not produce reactive oxygen species (ROS) themselves but induce ROS production in bacteria and accelerate bacterial death. Biocompatibility studies suggested that ZIFs have minimal toxicity to human cells, indicating their potential in biomedical applications. This research provides insights into the antibacterial mechanisms of ZIFs, which can support their development for antimicrobial use.