To evaluate and compare of the immunogenicity differences of flagellins FliC and FljB of Salmonella abortus equi, and lay the experimental foundation for the further utilization of the two recombinant proteins, FliC and FljB recombinant proteins were induced, expressed and purified. The purified FliC and FljB were used to immunize mice separately. The antibody level, titer and subtype of mice serum were detected after immunization. Immune-related receptors and histopathological changes were observed in immunized mice after challenged. The recombinant proteins FliC and FljB were successfully induced and expressed. Proteins of about 52 kDa and 42 kDa were purified. High levels of specific IgG antibodies were induced in mice immunized with these two proteins, the antibody level of FljB-immunized group was higher than that of FliC-immunized group, and IgG1 was the dominant subtype of antibody. The challenge protection rate of the FljB-immunized group was 87.5%, higher than that of FliC immunized group. Bacterial loads and observation pathological of FljB-immunized group were better than that of FliC immunized group, the levels of TCR2, TCR4, MHC-I and TCR induced by FljB-immunized group were higher than those of FliC-immunized group. The of immune response induced by FljB group was better than that of FliC group.