Many recent studies have shown that flagellin fused to heterologous antigens can induce significantly enhanced humoral and cellular immune responses through its adjuvant activity. Therefore, in this study, two key B cell epitopes and a truncated VP1 (VP1) protein from foot-and-mouth disease virus (FMDV) were expressed as flagellin fusion proteins in different patterns. Specifically, VP1 and two duplicates of two key B cell epitopes (2xB1B2) were fused separately to the C-terminus of flagellin with a universal exogenous T cell epitope to construct FT (Flagellin-Truncated VP1) and FME (Flagellin-Multiple Epitopes). In addition, the D3 domain of flagellin was replaced by VP1 in FME, yielding FTME (Flagellin-Truncated VP1-Multiple Epitopes). The immunogenicity and protective efficacy of the three fusion proteins as novel FMDV vaccine candidates were evaluated. The results showed that FT, FME, and FTME elicited significant FMDV-specific IgG responses at 10g/dose compared with the mock group (P<0.05), with FTME producing the highest response. No significant differences in the antibody response to FTME were observed between different immunization routes or among adjuvants (ISA-206, poly(IC), MPLA, and CpG-ODN) in mice. In addition, at 30g/dose, all three fusion proteins significantly induced neutralizing antibody production and upregulated the levels of some cytokines, including TNF-, IFN-, and IL-12, in guinea pigs. Importantly, all three fusion proteins provided effective protective immunity against FMDV challenge in guinea pigs, though different protection rates were found. The results presented in this study indicate that the FTME fusion protein is a promising novel vaccine candidate for the future prevention and control of foot-and-mouth disease.