The myofibrillar protein (MP) of duck meat is prone to excessive oxidation during thermal processing, resulting in a decline in its overall quality. In this paper, the effect of shikimic acid on the oxidative structure of duck muscle fibrin was studied. The findings showed that, at a mass ratio of 1:50,000 (g/g) between shikimic acid and MP, the carbonyl content of MP was reduced by 74.20%, while the sulfhydryl content was increased by 73.56%. MP demonstrated the highest denaturation temperature, whereas its thermal absorption was the lowest. The percentage of α-helixes and β-sheets increased by 16.72% and 24.74%, respectively, while the percentage of irregular structures decreased by 56.23%. In addition, the surface hydrophobicity index of MP exhibited a significant decrease (p < 0.05), while there was a significant increase in its free radical-scavenging ability (p < 0.05). Molecular fluorescence spectrum analysis showed that shikimic acid could bind to MP, altering the internal environment of MP and enhancing its thermal stability. FTIR analysis showed that shikimic acid could enhance the distribution of protein particle sizes by reducing irregular structures, the proportion of β-rotation, and the degree of protein aggregation. It is hoped that this research can offer scientific support for improving meat processing technology.