The invention relates to the technical field of biomedicine, and particularly provides a fusion protein of an SVV and an FMDV, an encoding gene of the fusion protein, an expression vector, a cell line, engineering bacteria, a vaccine and application. The fusion protein is obtained by replacing an epitope capable of inducing the body to produce a neutralizing antibody with a decoy epitope and comprises SVV VP1 protein fragments, FMDV VP1 protein fragments and complement C3d protein fragments. The fusion protein combines antigens for inducing the body to produce the neutralizing antibody, of twopathogens of SVV and FMDV, and the safety of the antigens is improved while the antigenic epitopes of the SVV and the FMDV are reserved. The complement C3d molecules can excite nonspecific body fluidand cellular immune reactions in the body, and play an important role in increasing the antibody titer of the vaccine, and activating the cellular immune response of the body. The vaccine prepared bymeans of the fusion protein is safe and effective, and hydroa and foot-and-mouth diseases can be effectively prevented.