Vaccines are of great importance to green aquaculture. In this study, the polyvalent immunoprotective activities of protein, DNA and egg yolk antibody (IgY) vaccines of Vibrio fluvialis outer membrane protein VF08100 were assessed. Carassius auratus was immunized with these three vaccines and challenged with V. fluvialis and Aeromonas hydrophila. The results showed that the three vaccines had significant immune protection rates (p <
0.01) against V. fluvialis and A. hydrophila infections, could activate the congenital immune response in C. auratus, and downregulate the expression of inflammation genes (p <
0.01) and antioxidant factors (p <
0.01) to reduce the inflammatory response and antioxidant reactions, respectively. Moreover, the three vaccines could protect the internal tissue structure integrity and reduce the apoptosis and DNA damage of kidney cells induced by bacterial infection. Therefore, the protein, DNA and IgY vaccines of VF08100 resisted multiple bacterial infections and can be used as polyvalent candidate vaccines for aquaculture.