Nanovaccines based on self−assembling nanoparticles (NPs) can show conformational epitopes of antigens and they have high immunogenicity. In addition, flagellin, as a biological immune enhancer, can be fused with an antigen to considerably enhance the immune effect of antigens. In improving the immunogenicity and stability of a foot−and−mouth disease virus (FMDV) antigen, novel FMDV NP antigens were prepared by covalently coupling the VP1 protein and truncated flagellin containing only N−terminus D0 and D1 (N−terminal aa 1–99, nFLiC) with self−assembling NPs (i301).The results showed that the fusion proteins VP1−i301 and VP1−i301−nFLiC can assemble into NPs with high thermal tolerance and stability, obtain high cell uptake efficiency, and upregulate marker molecules and immune−stimulating cytokines in vitro. In addition, compared with monomeric VP1 antigen, high−level cytokines were stimulated with VP1−i301 and VP1−i301−nFLiC nanovaccines in guinea pigs, to provide clinical protection against viral infection comparable to an inactivated vaccine. This study provides new insight for the development of a novel FMD vaccine.