Abstract: Objective The case involving human infection with pathogenic avian influenza A (H9N2) was identified. The full nucleotide sequence of the H9N2 virus was generated with next-generation sequencing and the sequence was evaluated on potential pandemic risk. Methods The full nucleotide sequence of the H9N2 virus was generated with next-generation sequencing Miseq system. Phylogenetic trees were constructed based on full-length nucleotide sequence of the eight genes to characterize functional amino acid motifs. Results The phylogenetic trees showed that the HA gene of H9N2 was in Eurasian lineage I, gene M in G1-like lineage and gene PB2 in G9-like lineage. NA formed a monophyletic clade in the external gene tree. PB1, PA, NP, NS were in the SH/F/98-like lineage. The cleavage site in HA gene was PSRSSR/GLF. The amino acid of receptor binding position 226 in HA was the Leucine (L). Three amino acids (sites 63-65) were deleted at the NA stalk region. The genes didn't mutate in position of L336M in PA, Q591R and E627K in PB2, which might improve the adaptability of the virus once mutated. But genes mutated in position of N30D and T215A in M1, L89V in PB2 and P42S in NS1, which might increase virulence. Except for S31N in M2 the potential antibiotic-resistant positions E119G, R152K, H274Y and R292K in NA, L26F, V27A, A30T, S31N, and G34E in M2 didn't mutate. eight glycosylation motifs in HA and eight in NA were changed, in which seven motifs and five motifs were in high degree of reliability, respectively. Conclusions Most key motifs in the H9N2 were relatively conservative. This H9N2 strain might not cause pandemic risk, while far more were needed in the dynamic molecular evolution monitoring.