Objective To investigate the evolutionary characteristics and important amino acid sites of the neuraminidase (NA) gene of the novel influenza virus A/H7N9 in 2013 epidemic. Methods The NA gene sequences of influenza virus A N9 subtype of different times and areas were downloaded from the database of The National Center for Biotechnology Information (NCBI) and The Global Initiative on Sharing All Influenza Data (GISAID). MEGA 5.05 and BioEdit softwares were used for phylogenetic tree construction and nucleotide/protein sequence analysis. Results The NA gene sequence of the novel influenza virus A/H7N9 in 2013 shared a 96% similarity with that of the H11N9 avian strain found in Czech Republic in 2010. There were 5 amino acid deletions in this novel influenza virus, and one of the new strains had a variation in potential enzymatic active sites. Conclusion The NA gene of this 2013 novel influenza virus might originate from the avian H11N9 strains detected in Czech Republic. The deletion of amino acid might result in human infection and high fatality rate.