Influenza A(H3N2) virus exhibited complex seasonal patterns to evade pre-existing antibodies, resulting in changes in the antigenicity of the viron surface protein hemagglutinin. To monitor the current circulating influenza viruses as well as to assess the capacity of health emergencies in Shanghai port, we collected respiratory specimens of passengers from different countries and regions including some of Europe with influenza-like illness in Shanghai port during 2016/17 and examined to amino acid substitutions and calculated the perfect-match vaccine efficacy using the p epitope model. Phylogenetic analysis of HA gene revealed that Influenza A(H3N2) viruses belonging to eight clades were detected, and three amino acid substitutions in subclade 3C.2a.4 were also added. Besides, there were two epidemic influenza virus strains circulating in the 2016/17 winter season and 2016 summer season. The results of lower predicted vaccine effectiveness in summer (0.1864) suggest that A(H3N2) strains circulating in 2016 summer was not a good match for the A/Hong Kong/4801/2014 vaccine strain. So, Shanghai port owns the advantage of grasping the risk of international spread of influenza in the first time, and curbing the entry of A(H3N2) from abroad at the earliest stage of the current influenza pandemic.