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Aeromonas hydrophila is a widespread fish pathogen. However, due to the extensive use of antibiotics in aquaculture, this bacterium has developed drug resistance. In recent years, tea tree oil, extracted from Melaleuca alternifolia, has gained widespread application in antibacterial research. Nevertheless, the underlying mechanism of action of tea tree oil on A. hydrophila remains unclear. In this study, the inhibitory effect of tea tree oil on A. hydrophila was analyzed, and its mechanism of action was elucidated through a combination of transcriptome and proteome analyses. In the current work, tea tree oil (0.039 mg/mL) significantly inhibited the growth of A. hydrophila and changed the permeability of the cell membrane. A total of 109 differentially expressed genes (DEGs) were identified by the combined analysis of the transcriptome and the proteome, of which 46 were upregulated and 63 were downregulated. These co-regulated DEGs were primarily enriched in metabolic pathways such as bacterial chemotaxis, pyrimidine metabolism, and the two-component system. Simultaneously, it was found that the target proteins of tea tree oil, such as secB, yajC, rpsP, rplL, and rpsT were significantly downregulated. These findings suggested that the potential of tea tree oil as an alternative to antibiotics in inhibiting the growth of A. hydrophila. It provides new insights into the molecular mechanisms underlying the antimicrobial activity of tea tree oil against A. hydrophila.