B2 haplotype MHC has been extensively reported to confer resistance to various avian diseases. But its peptide-binding motif is unknown and the presenting peptide is rarely identified. Here, we identified the peptide-binding motif of B2 haplotype MHC Ⅰ molecules (X-A/V/I/L/P/S/G-X-X-X-X-X-X-V/I/L) in vitro using Random Peptide Library-based MHC-Ⅰ LC-MS/MS analysis. To further clarify the structure basis of the peptide binding motif, we determined the crystal structure of the BF2*02:01-PB2552-560 complex at 1.9 ? resolution. We found that BF2*02:01 had a relatively wide antigen-binding groove, and the structural characterization of pockets of BF2*02:01 was consistent with the characterization of peptide-binding motif. The wider features of the peptide-binding motif and increased number of peptides bound by BF2*02:01 than BF2*04:01 might resolve the puzzles for the presence of potential H9N2 resistance in B2 chickens. Afterwards, we explored the H9N2 AIV-induced cellular immune response in B2 haplotype chickens in vivo. We found that ratio of CD8+ T cell and kinetic expression of cytotoxicity genes including Granzyme K, IFN-γ, NK lysin, and PARP in PBMCs were significantly increased in defending against H9N2 AIV infection. Especially, we selected 411 epitopes as candidate epitopes based on the peptide-binding motif and further identified four CD8+ T-cell epitopes on H9N2 AIV including NS198-106, PB2552-560, NP182-190, and NP455-463 via ELI-spot IFN-γ detections after stimulating memory lymphocytes with peptides. More importantly, these epitopes were found to be conserved in H7N9 AIV and H9N2 AIV. These findings provide direction for developing effective T cell epitope vaccines using well-conserved internal viral antigens in chickens.