SummaryThe study aimed to assess the in vitro antibacterial effect of thymol (Thy) in conjunction with ultrasound (US) on Shewanella putrefaciens (S. putrefaciens). The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of Thy against S. putrefaciens were 0.50 and 1.00 mg mL−1, respectively. US was found to augment the antibacterial efficacy of Thy, resulting in a significant reduction of 2.36 log CFU mL−1 in the total colony count of S. putrefaciens, ensuring that the bacterial population maintained a consistently low growth rate. Quantitative detection of crystal violet revealed that the combined treatment exhibited a pronounced inhibitory effect on biofilm formation, with a clearance rate of mature biofilms reaching 91.60%. Alkaline phosphatase (AKPase), lactate dehydrogenase (LDHase), UV absorbing substance permeability, and other indicators were employed to measure changes in the bacterial cell membrane and internal environment. Scanning electron microscopy (SEM) was further used to observe the bacteria morphology before and after treated by US and Thy, a notable collapse of bacterial cells was observed, accompanied by ruptured outer membranes, damaged cell walls, and extensive leakage of cellular contents. This study presents a novel approach for controlling bacterial growth in food preservation methods.