Objective To study B cell epitopes of the influenza virus hemagglutinin (HA) by computer simulation and ELISA blocking experiment, and to establish a new method for pathogen microbial epitope detection. Methods The 2009 H1N1 influenza virus inactivated vaccine was used as the immunogen, and the monoclonal antibodies (mAbs) were prepared by conventional hybridoma fusion and screening techniques. The characteristics of mAbs were identified by ELISA, hemagglutination inhibition (HI) and Western blot analysis. The obtained mAbs were used as a tool to predict the epitope of H1N1 influenza virus by ELISA blocking experiment combined with computer simulation method. Results Four mAbs against the HA antigen on H1N1 influenza virus were obtained, and HA epitopes were classified into two types by ELISA blocking experiment. The computer simulation revealed that the four antibodies could bind to two epitopes on HA. Conclusion The results of computer simulation and ELISA blocking experiment are consistent, and a new method for predicting the epitopes of other pathogenic microorganisms had been established.