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As a popular marine saccharide, chitooligosaccharides (COS) has been proven to have good antioxidant activity. Its antioxidant effect is closely related to its degree of polymerization, degree of acetylation and sequence. However, the specific structure–activity relationship remains unclear. In this study, three chitosan dimers with different sequences were obtained by the separation and enzymatic method, and the antioxidant activity of all four chitosan dimers were studied. The effect of COS sequence on its antioxidant activity was revealed for the first time. The amino group at the reducing end plays a vital role in scavenging superoxide radicals and in the reducing power of the chitosan dimer. At the same time, we found that the fully deacetylated chitosan dimer <b>DD</b> showed the strongest DPPH scavenging activity. When the amino groups of the chitosan dimer were acetylated, it showed better activity in scavenging hydroxyl radicals. Research on COS sequences opens up a new path for the study of COS, and is more conducive to the investigation of its mechanism.