Influenza A (H3N2) virus has a faster evolution rate than other types of influenza viruses. In this study, whole genome sequencing was performed to better understand the molecular evolution of influenza H3N2 and the protective effect of influenza virus vaccine in Qinghai Province, China, in 2017. Complete sequences of eight gene segments of two seasonal influenza H3N2 isolates were sequenced and analyzed using DNASTAR and MEGA 6.06 software. Additionally, the three-dimensional structure of the HA protein was predicted using the SWISS-MODEL server. Phylogenetic and amino acid sequence analysis revealed that two Qinghai H3N2 isolates were typical low-pathogenic influenza viruses, and were relatively closely related to the 2016-2017 vaccine strain, 3C.2a-A/Hong Kong/4801/2014. The presence of several antigenic site substitutions (T131K, G/R142K, K160T and R261Q in the HA protein) were specific for the two Qinghai H3N2 virus strains. In addition, amino acid substitution of K160T at the glycosylation site of HA and H75P in PB1-F2 in Qinghai isolates might affect the antibody binding ability and virulence of the influenza virus. The presence of several antigenic site mutations in the Qinghai H3N2 isolates confirmed the evolution of circulating H3N2 strains.“,”Influenza A (H3N2) virus has a faster evolution rate than other types of influenza viruses. In this study, whole genome sequencing was performed to better understand the molecular evolution of influenza H3N2 and the protective effect of influenza virus vaccine in Qinghai Province, China, in 2017. Complete sequences of eight gene segments of two seasonal influenza H3N2 isolates were sequenced and analyzed using DNASTAR and MEGA 6.06 software. Additionally, the three-dimensional structure of the HA protein was predicted using the SWISS-MODEL server. Phylogenetic and amino acid sequence analysis revealed that two Qinghai H3N2 isolates were typical low-pathogenic influenza viruses, and were relatively closely related to the 2016-2017 vaccine strain, 3C.2a-A/Hong Kong/4801/2014. The presence of several antigenic site substitutions (T131K, G/R142K, K160T and R261Q in the HA protein) were specific for the two Qinghai H3N2 virus strains. In addition, amino acid substitution of K160T at the glycosylation site of HA and H75P in PB1-F2 in Qinghai isolates might affect the antibody binding ability and virulence of the influenza virus. The presence of several antigenic site mutations in the Qinghai H3N2 isolates confirmed the evolution of circulating H3N2 strains.