To investigate the bactericidal efficacy of Thymus mongolicus essential oil, Origanum vulgare essential oil and Cinnamomum cassia essential oil on Photobacterium damselae subsp. damselae (PDD), an important pathogenic bacteria in mariculture, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of these essential oils against six PDD strains with different pathogenicity were determined through double dilution method. These strains' growth curve after adding plant essential oil was detected using spectrophotometry. The expression of virulence genes and activity of extracellular products (ECP) under different essential oil concentrations in two highly pathogenic PDD strains were analyzed. Meanwhile, the bactericidal efficacy of the plant essential oils after long-time storage and metal ions addition were studied. The results showed that the three plant oils had good bactericidal effects on the six PDD strains, with MICs of 32-128 μg/mL and MBCs of 64-192 μg/mL. They had good inhibitory effects on the expression of virulence genes, phospholipase activity and hemolytic activity of ECP in two highly pathogenic PDD strains. Specifically, low concentration of plant essential oil exhibited significant inhibitory effects on the expression of virulence genes. After 35 days of storage away from light, the sterilization rates of the three essential oils remained above 99%, demonstrating excellent pharmacodynamic stability. The presence of different concentrations of Na⁺, Mg²⁺, Ca²⁺, K⁺ in the water environment did not exert a significant influence on the bactericidal efficacy of the three essential oils. The results showed the suitability of the three essential oils for the development of novel drugs or feed additives in aquaculture, with potential application in disease prevention and treatment. This study can provide reference for expanding the application of aromatic plant essential oil in the prevention and control of aquatic diseases.