This study aimed to establish the method of expression and purification of EsxB protein, explore the EsxB antibody-positive Staphylococcus aureus (S. aureus) clinical infection status and relevance of drug resistance. Constructed EsxB prokaryotic expression system by homologous recombination, Ni(2+) column was used to purify EsxB protein; and then ELISA was used to detect the anti-EsxB antibodies in serum of 78 patients with S. aureus infection; antimicrobial susceptibility of related S. aureus strains by automatic bacterial identification analyzer. EsxB prokaryotic protein expression system was constructed and EsxB protein was purified successfully; anti-EsxB antibodies were present in the serum of patients with S. aureus infection up to 28.21% (22/78). The proportion of multi-drug resistant and Methicillin-resistant S. aureus strains isolated from anti-EsxB antibodies positive patients were 100.0% (22/22), 77.3% (17/22), respectively, which were statistically higher than those strains isolated from anti-EsxB antibody-negative patients (35.7% (20/56) and 21.4% (12/56), respectively) (all P values < 0.01). Method for expression and purification of EsxB protein was established. All the S. aureus strains isolated from EsxB antibody-positive patients were multidrug resistant strains and most of them were resistant to methicillin.