Abstract: The aim of this study was to elucidate the antibacterial mechanism of Zanthoxylum bungeanum extract against Shewanella putrefaciens. The effects of the extract on bacterial growth, cell wall integrity, membrane permeability, cellular morphology, and transcriptional processes were investigated using growth curve analysis, extracellular alkaline phosphatase (AKP) and protein leakage assays, transmission electron microscopy, DNA-binding analysis, and transcriptomics. The results demonstrated that Zanthoxylum bungeanum extract significantly inhibited Shewanella putrefaciens growth in a concentration-dependent manner. It disrupted the integrity of the cell wall and membrane permeability, leading to the leakage of AKP and intracellular proteins. Additionally, the extract interacted with Shewanella putrefaciens genomic DNA, altering metabolic pathways, signal transduction, and motility-related gene expression. Transcriptome analysis identified 301 differentially expressed genes, with the flagellar assembly pathway exhibiting the most significant enrichment （P<0.05）. These findings indicated that Zanthoxylum bungeanum extract exerted its antibacterial effects through multifaceted mechanisms, including growth suppression, structural damage to the cell wall and membrane, morphological deformation, and transcriptional modulation. Therefore, it is a promising natural resource for developing antibacterial agents.