The aim of the study is through observing the morphology of the prepared influenza virus (H1N1) with transmission electron microscopy (TEM) and atomic force microscopy (AFM) to explore the application of AFM on the research of the external character of viruses and provide a new, simple and efficient technique for the study of the viral morphology. TEM image was obtained by negatively stained influenza virus with 1% Phosphotungstic Acid; AFM image applied the tapping mode to influenza virus without any further treatment in air at room temperature, and the morphology parameters, including length (diameter), Ra and Rq are calculated by sectional analysis. The shapes of influenza virus A are spherical, filamentous or other pleomorphous particles observed by both AFM and TEM. TEM image of influenza virus A is two-dimensional image, and viral surface has visible spikes, while AFM exhibits the three-dimensional image that can be described with several quantifiable indexes through sectional analysis. AFM phase images show viral surface clearly which is characterized by rugged feature and gear-like protuberance. As compared with TEM, AFM is a new research tool for viral morphology study with the advantages of simple sample preparing, visible interface and is intuitionistic for researchers. The surface characteristic parameters of viruses provided by AFM can be served as the main quantifiable indexes for viral morphological study.