The H9N2 avian influenza virus (AIV) is difficult to prevent and control because of its low pathogenicity and frequent mutation. In a previous study, the HA (hemagglutinin) protein of H9N2 was expressed in a rice endosperm reactor and prepared into a subunit vaccine to immunize chickens and mice, both of which exhibited a good immunity effect. The results of the intermediate tests of the transgenic strains (AIV-1 and AIV-3) showed that the HA gene can be stably expressed. Agronomic traits, such as plant height and number of grains, were significantly optimized in the transgenic strains. Moreover, no exogenous HA genes were found in the leaves of the weeds, and it was initially determined that there was no risk of gene drift. This study provides key technical support for the commercialization of plant subunit vaccines for avian influenza viruses.