Provided is an influenza mucosal vaccine composition and preparation and application thereof. This composition contains an antigen fusion protein which includes an influenza virus antigen and a Type IIb heat-labile enterotoxin A subunit from Escherichia coli. Immunization with this antigen fusion protein induces cellular and humoral immune responses, including systemic and mucosal immune responses, against a specific influenza virus in a subject, and therefore protects the subject from viral infection.