The expression patterns of TLR18, MyD88, and corresponding ligand TRAF6, downstream factor IRF5, and P65 in spleen tissues of breeding strain F₄ and German mirror carp were determined by RT-PCR. The difference of related genes in disease resistance mechanism between breeding strain F₄ and German mirror carp was analyzed. The results show:the expression of TLR18, MyD88, TRAF6, and IRF5 showed the same trend between the two groups, which increased first, then decreased and stabilized, and reached the highest at 48 h, while the relative expression of P65 in non-breeding strain increased first, then decreased and recovered to the initial level, and reached the highest at 48 h. In breeding strain, the expression trend decreased and then recovered to the initial level. The relative expression of TLR18 and IRF5 in breeding strain was significantly lower than that in the non-breeding strain without CyHV-3 infection. The relative expression levels of MyD88, TRAF6, and P65 in breeding strain were significantly higher than those in non-breeding strain. At the early stage of CyHV-3 infection, the relative expression levels of TLR18 and P65 in breeding strain were significantly lower than those in non-breeding strain, while the relative expression levels of MyD88, TRAF6, and IRF5 in breeding strain were significantly higher than those in non-breeding strain. It is speculated that during CyHV-3 infection, TLR18 generateed IRF5 by binding to TRAF6 through the MyD88 pathway, which cleared the virus and activated the NF-κB signaling pathway to produce inflammatory factors. In breeding strain, more IRF5 was produced and the NF-κB signaling pathway was not significantly activated to resist the virus. This result may be related to breeding. These results not only verified the improvement of CyHV-3 resistance in breeding strain in the body basic condition and innate immunity but also laid a foundation for further study of the role of fish TLRs in the process of virus infection and related signaling pathways.