Intranasal vaccination is a desired route for protection against influenza viruses by mucosal and systemic immunity. However, the nasal mucosa impedes the intranasal delivery of vaccines. Here, we formulated layer-by-layer (LBL) influenza vaccine nanoparticles for effective intranasal delivery by coating them with alternating mucoadhesive cationic chitosan and muco-inert anionic CpG adjuvants. The nanoparticle cores were formed by desolvating influenza M2e antigen and coating it with hemagglutinin (HA) antigen via biotin-streptavidin conjugation. LBL modification promoted nasal delivery and interaction with the resident immune cells. Intranasal administration with LBL nanoparticles significantly improved cellular and humoral immune responses against HA and M2e including high IgA titers, a hallmark of potent mucosal immunity and persistence of immune responses. Distinct trends for antigen-specific immune responses were observed for different routes of vaccination. The enhanced immune responses conferred mice protection against the influenza challenge and prominently reduced viral titers, demonstrating the effectiveness of intranasal LBL vaccine nanoparticles.