Some subtypes of avian influenza A viruses (IAVs) have been associated with human infections (e.g. H3N8, H5Ny, H7Ny, H9N2, and H10Ny), and the ability of these viruses to cause zoonotic infections further increases the public health risk of avian IAVs. Among them, H9N2 virus is one of particular importance, both in its own right and as a contributor of internal gene segments to other emerging zoonotic avian IAVs. In recent years, an increasing number of H9N2 strains have been observed to be highly pathogenic in mice without prior adaptation. In this study, we found that a naturally occurring H9N2 isolate, A/chicken/Jiangxi/198/2019 (JX198), is lethal in mice. To investigate the molecular basis for the high virulence of JX198 in mice, a series of reassortants and mutants were generated and tested. We found that the PA, especially D347G mutation in PA, is responsible for the increased pathogenicity of JX198 in mice. Notably, D347G in PA of JX198 significantly alters the polymerase activity, vRNA production, and plaque-formation. Thus, our data demonstrate that a novel molecular marker, D347G in PA, determines the virulence of H9N2 in mice, posing a potential risk of H9N2 with D347G in PA for public health and highlighting the significance of continuing surveillance of H9N2 field strains.