Background Infective endocarditis, a disease with high mortality and morbidity, is most commonly caused by Staphylococcus aureus; mortality and morbidity further increase in the presence of methicillin-resistant strains of S. aureus. Linezolid is the first of the oxazolidinones, a new antibiotic group that has been approved for the treatment of infections caused by gram-positive cocci. Linezolid reduces the quantity of microorganisms in vegetation to some extent; in addition, the use of hyperbaric oxygen (HBO) and ozone (O3) therapies is likely to improve targeted antibacterial effect. Materials and methods Fifty-six adult male Wistar rats weighing 300-350 g were used. The subjects were divided into groups as follows: Group 1 (n = 8): control group that was not inoculated with microorganisms and was untreated; Group 2 (n = 8): control group that was inoculated with microorganisms but was untreated; Group 3 (n = 8): linezolid treatment group; Group 4 (n = 8): O3 therapy group; Group 5 (n = 8): HBO therapy group; Group 6 (n = 8): linezolid + O3 therapy group; Group 7 (n = 8): linezolid + HBO therapy group. Results In terms of reducing the number of colonies in the aortic valve, linezolid + HBO therapy was found to be the most effective treatment. Then, respectively linezolid + O3, linezolid, HBO, and O3 were found to be effective. Conclusions We found that linezolid significantly reduced the number of bacteria in the vegetation in the experimental endocarditis model, and HBO therapy increases the effectiveness of linezolid and makes this better than O3.