This study aimed to elucidate the antibacterial mechanism and antibiofilm activity of ginger essential oil (GEO) against Shewanella putrefaciens. On the basis of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC), alkaline phosphatase (AKPase), succinate dehydrogenase (SDH), and glucose‐6‐phosphate dehydrogenase (G6PDH) activities were analyzed to evaluate the damage degree of S. putrefaciens on cell wall and membrane, and the microstructure was observed by scanning electron microscope (SEM) to evaluate the action effect against S. putrefaciens. The results showed that the MIC and MBC of GEO against S. putrefaciens were 27.8125 mg/mL and 55.625 mg/mL, respectively. The surface structures and cell membrane of S. putrefaciens were rigorously damaged by 1 MIC and 2 MIC GEO, leading to the leakage of cellular nucleic acids, protein, and β‐galactosidases from the bacterial cells. GEO could not only decrease the biomass of biofilm but also remove mature biofilm. In addition, GEO could reduce the production of exopolysaccharides and extracellular proteins, and could lessen the metabolic activity of biofilm cells. These results demonstrated that GEO exhibited efficient antibacterial characteristics against S. putrefaciens, which could act as a natural antibacterial and antibiofilm agent on the preservation of aquatic products.