RNAs isolated from the foot-and-mouth disease virus strain AF72 were used as templates for RT-PCR to amplify the target gene. The PCR products purified were cloned into the pGEM-T easy vectors and transformed into E. coli JM109. The positive recombinant plasmids were identified by electrophoresis, PCR, and restriction digestions with Spe I and Spe I analysis. The nucleotide sequences were confirmed by comparing with the full-length sequence of the other reference strains. The 3D model of structure protein VP3 of FMDV strain AF72 was obtained using homology modeling. On the basis of several parameters, such as hydrophilicity, flexibility, antigenic index, and surface probability, the B cell epitopes on VP3 were predicted. After analyzing the difference among VP1, VP2, VP3, VP4, at the nucleotide level, the mutation rates of these four encoding sequences were no difference (P > 0.05), however, at the amino acid level, those mutation rates were different (P < 0.05). The regions of 1th~24th、24th~35th、36th~42th、45th~56th、65th~122th、124th~172th、177th~210th、and 211th~219th in VP3 protein are most probably conservative. The 3D mold could be divided into A, B and C regions, the conformation of the VP3 of FMDV strain AF72 was regular, and the B-cell epitopes in VP3 probably exist in the following regions: 18 aa~23 aa, 30 aa~44 aa, 60 aa~75 aa, 113 aa~124 aa, 130 aa~142 aa, and 193 aa~220 aa. This result offers valuable information for design of FMDV multi-epitope vaccine against FMDV.