Objective  To analyze the correlation between the complete genomic sequence of prevalent strains of influenza virus H3N2 and clinical characteristics. Methods  Nasal swab samples of patients with respiratory tract infection collected from December 2014 to March 2015 were used to perform the complete genomic sequencing for strains of influenza virus H3N2 after PCR amplification. Characteristics of nucleic acid sequence and amino acid variations were analyzed. Results  Compared with reference strains of 2014-2015 influenza virus strains recommended by WHO, the epitope of HA1 protein of 14 strains from different patients varied. For hosts with significant structural changes of epitope, their body temperature was higher and clinical manifestations were severer. The amino acid E190D of HA1 protein of all 14 strains varied. A new glycosylation site appeared in NA protein of 6 strains. One strain has the V27A variation of M2 protein that caused the amantadine resistance. All 14 strains had the I18T variation of PB1-F2 protein. Conclusion  Drug resistance variation of M2 protein and amino acid variation of PB1-F2 protein suggest that isolated strains of influenza virus H3N2 have combined with gene fragments of influenza virus H1N1 during the course of evolution. The increase of variations of the epitope of HA1 protein may cause stronger immune response of patients.