Aeromonas hydrophila is one of the major conditional pathogens causing loss in freshwater aquaculture, with strong drug resistance. Tea tree oil (TTO) can be a good alternative to antibiotics to achieve bacteriostatic effect against A. hydrophila. In this study, an in vitro bacterial inhibition assay was used to evaluate the inhibitory mechanism of TTO against A. hydrophila by detecting the minimum inhibitory concentration (MIC), growth and inhibition curves, cell membrane integrity, bacterial death, and transcriptome sequencing analysis. The results showed that the MIC of TTO against A. hydrophila was 39 μg/mL. Meanwhile, TTO significantly altered the cell membrane permeability and biofilm formation, which in turn increased the concentration of intracellular K+ and DNA exocytosis, and ultimately led to the death of A.hydrophila. Transcriptional sequencing revealed that TTO significantly altered both bacterial chemotaxis and two-component system (TCS) pathways in KEGG enrichment (P < 0.05), which are related to intracellular survival, growth, motility, virulence and environmental stress response. In addition, Outer membrane porin (OmpA), serine protease (ahpA), repeat in toxin A (rtxA), temperature-sensitive Protease (eprCAI), adhesin (aha) and aerolysin (aerA) mRNA levels decreased (P < 0.05). In summary, 1 MIC TTO can prevent bacterial colonisation in host tissues by disrupting the integrity of the membrane structure of A. hydrophila, reducing the activity and environmental resistance of serine proteases and other extracellular proteases to prevent bacterial colonisation, and thus reducing the survivability of A. hydrophila to achieve its bacteriostatic effect. It will provide a theoretical basis for the wide application of TTO in aquaculture.