Sarcoplasmic calcium-binding protein (Cra a 4) from Crassostrea angulata belongs to the EF-hand superfamily, and understanding of its structure−allergenicity relationship is still insufficient. In this study, chemical denaturants were used to destroy the structure of Cra a 4, showing that disruption of the structure reduced its IgG-/IgE-binding activity. To explore which critical amino acid site affects the allergenicity of Cra a 4, the mutants were obtained by site-directed mutations in the disulfide bonds site (C 97 ), conformational epitopes (I 105 , D 114 ), or Ca 2+ -binding region (D 106 , D 110 ) and their IgG-/IgE-binding activity was reduced significantly using serological tests. Notably, C 97 A had the lowest immunoreactivity. In addition, two conformational epitopes of Cra 4 were verified. Meanwhile, the increase of the α-helical content, surface hydrophobicity, and surface electrostatic potential of C 97 A affected its allergenicity. Overall, the understanding of the structure−allergenicity relationship of Cra a 4 allowed the development of a hypoallergenic mutant.