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The effective prevention of plant bacterial infections has been complicated and challenged by unceasing bacterial resistance. The application of traditional bactericides has achieved certain effects to alleviate this situation. However, these chemicals also have limitations, such as short half-life in reality, limited bioavailability, and pollutant emission from their formulations. These disadvantages drive the demand for promoting antibacterial therapeutics. Self-assembled nanostructures based on amphiphiles have inherently versatile characteristics, including high durability, good bioavailability, sustained release, and regenerability. As such, they have garnered wide interest because of these advantages that may serve as a feasible platform for the management of pathogenic infections. Flexible tuning of the shapes of these nanostructures by manipulating noncovalent driving forces consequently results in different levels of antibacterial activity. Herein, an antibacterial amphiphile, 1-[11-(9-anthracenylmethoxy)-11-oxoundecyl]pyridinium bromide (AP), was assembled into microfilms in screening medium. Hierarchical nanofibers were constructed by introducing an electron-deficient trinitrofluorenone (TNF) molecule into the assembling system directed by charge-transfer (CT) interactions to further investigate the contribution of aggregate shape to bioactivity. Biological evaluation revealed that antibacterial efficacy improved after CT complex formation. This study provides an innovative platform for developing versatile assembled structures for restraining the propagation of plant pathogens and an improved understanding of the actual interplay between the self-assembly and antibacterial ability of bactericides at the supramolecular level.