Objective To investigate the evolution and variations in coding amino acids of hemagglutinin (HA) gene of the novel avian influenza virus H7N9 in 2013 epidemic. Methods The HA gene sequences of influenza virus H7N9, H7N2, H7N3 and H7N7 subtypes 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 software was used for sequence analysis and N-J method was used for constructing the phylogenetic trees. The amino acid sequences at the receptor binding sites, glycosylation sites, and cleavage sites was aligned and analyzed. Results The HA genes this novel A/H7N9 virus in 2013 shared a 95.3%-95.6% similarity with JQ906573.1|Zhejiang (H7N3 virus) isolated in 2011. The most important variation in this novel H7N9 isolates was found at the receptor binding site: Q226L. The 5 glycosylation sites were highly conservative. One basic amino acid (R) at the HA cleavage sites, located between aa339 and aa340, was also found in this novel isolate. Conclusion The HA gene of this novel H7N9 isolate might originate from H7 subtypes carried by birds in China. The binding site change caused by Q226L variation might be responsible for human infection of this novel H7N9 isolate.