Vibrio parahaemolyticus was a foodborne pathogen that commonly found in seafood products and seriously threatened human food safety. Biofilm played a vital role in the resistance of V. parahaemolyticus, and the relationship between efflux pump encode gene vmeB and biofilm formation of V. parahaemolyticus remained poorly understood. In this study, the ATCC33846ΔvmeB deletion strain and ΔvmeB/pBAD33T-vmeB complement strain were constructed to reveal the mechanism that RND efflux pump vmeB gene regulated the biofilm of V. parahaemolyticus-mediated enrofloxacin resistance. The biofilm formation, motility and transcription levels related to outer membrane genes (ompA, ompH, ompN, ompU, ompV, ompW, ompX), flagella genes (fliA, fliC, fliS) and pilus genes (pilO, pilP) were explored. The results indicated that biofilm formation potential and motility were significantly decreased, the transcription levels of genes associated with the outer membrane, flagella, and pilus genes were significantly reduced in ATCC33846ΔvmeB. Additionally, Fourier transform infrared spectroscopy (FTIR) results demonstrated DNA integrity was compromised, protein structure was disrupted, and membrane lipid content was elevated in ATCC33846ΔvmeB. Meanwhile, ATCC33846ΔvmeB cells were observed to be damaged by scanning electron microscopy, and the flow cytometry analysis demonstrated a significant increase in cell apoptosis rate. Finally, the drug resistance results exhibited that the sensitivity of ATCC33846ΔvmeB to enrofloxacin is fivefold lower compared to ATCC33846. These results elucidate the drug resistance mechanism of vmeB regulates V. parahaemolyticus ATCC33846 biofilm, potentially providing new opportunities to develop inhibitors that specifically alter the characteristics of the biofilm matrix and thereby affect the enrofloxacin resistance of V. parahaemolyticus.