Abstract: Objective To understand the molecular evolution of HA genes and encoding amino acid sequence of influenza A (H1N1) pdm09 virus in Yichun in 2013, and provide scientific evidence for the prevention and control of the infection with influenza A (H1N1) pdm9 virus. Methods Eleven strains of influenza A (H1N1) pdm09 virus isolated in Yichun CDC influenza laboratory were randomly selected, and the virus RNA were extracted. The fragments of HA genes were amplified by using one-step RT-PCR and then sequenced. The nucleotide sequences and amino acid sequences of HA genes were analyzed with software DNAStar 7.0 and Mega 5.0. Results There was a high homology of HA genes between the 11 virus strains isolated in Yichun in 2013 and the vaccine strain A/California/07/2009 (H1N1) (GenBank:CY121680) recommended by WHO, HA did not have a large variation. The disulfide bonds and glycosylation sites of HA gene sequences did not mutate. Although there were 7 strains with simultaneously single site amino acid substitution mutation in the antigen determinant region A and the receptor binding site ring 130 or its vicinity, the new species variation with epidemiological significance did not form. Conclusion The vaccine of pandemic influenza H1N1 recommended by WHO still had certain protective effect. However, the variations of epitope region A and receptor binding site suggested that it is still needed to pay a close attention to the epidemic caused by influenza A (H1N1) pdm09 virus.