Objective To explore the differences in modeling influenza virus infection with two different respiratory tract infection modes in mice; and provide a reference for choosing the appropriate infection model for pathogenic research on influenza and developing vaccines and drugs. Methods The A/ Puerto Rico / 8 / 34 (H1N1) virus strain was selected to infect C57BL/ 6 mice by intranasal instillation and aerosol inhalation. The mice were weighed daily and their clinical symptoms were observed visually. Mice were killed on the 3rd, 7th, or 14th day after infection, and the lungs were weighed and used for virus assay, pathological observation and cytokine detection. Results Both infection modes successfully established an influenza virus infection model in a mouse, and their general trends of disease progression were similar. However, there are some differences in infection characteristics between the two models. Compared with the intranasal instillation group, weight loss occurred earlier in the aerosol inhalation group, and the lung index and viral load increased significantly on the 3rd day after infection (P< 0. 05). The lesion range and degree of inflammatory cytokine infiltration were also significantly increased in the aerosol group. Furthermore, the levels of cytokines interleukin( IL) -1α and IL-6 in the lung increased significantly on the 3rd and 7th days after infection, and tumor necrosis factor-α increased significantly on the 7th day (P< 0. 05). Conclusions Both modes of infection established a model of influenza in the mouse,but aerosol inhalation caused more obvious inflammatory infiltration and cytokine expression in the lung at an early stage of infection. The aerosol inhalation mode led to a more ideal animal model of influenza virus infection.