Vibrio parahaemolyticus is a food-borne pathogenic microorganism that commonly exists in aquatic products. In this study, the antibacterial activities of benzyl isothiocyanate (BITC) against V. parahaemolyticus were investigated by both transcriptomic analysis and morphological verification. Treatment with 1/8 minimum inhibitory concentration (1/8 MIC) BITC resulted in 234 upregulated genes and 273 downregulated genes. We selected six virulence genes that were significantly downregulated and verified them using quantitative real-time reverse transcription-polymerase chain reaction. The verification results revealed that the relative expression levels of the six genes VP0820, VP0548, VP2233, VPA2362, fliA and fliG were only 31.0%, 31.1%, 55.8%, 57.0%, 75.3%, and 79.9% of the control group, respectively. Among them, genes VP2233, fliA and fliG are related to flagella and VP2362 can regulate a protein relevant to biofilm formation. Morphologically, we verified that the swimming diffusion diameter of V. parahaemolyticus was significantly reduced by 14.9%, and biofilm formation was significantly inhibited by treatment with 1/8 MIC BITC. These results indicated that 1/8 MIC BITC had antibacterial effect on V. parahaemolyticus by inhibiting virulence gene expression related to flagella and biofilm. These findings are helpful to further elucidate the bacteriostatic mechanism of BITC on V. parahaemolyticus and other food-borne pathogens.