Mizuhopecten yessoensis is a nutritious, low-fat, high-value shellfish that contains a lot of protein, mainly myofibrillar protein (MP). Alginate oligosaccharides are low-molecular-mas, highly water-soluble marine oligosaccharides, which have immunoregulatory, antioxidant, hypoglycemic and lipid-lowering properties. This study aimed to investigate the effects of an enzymatic hydrolysate of alginate oligosaccharides at a concentration of 0.45 g/100 mL on the in vitro digestion characteristics, structure and physicochemical properties (intrinsic fluorescence spectrum, UV absorption spectrum, reactive sulfhydryl content, and surface hydrophobicity) of scallop myofibrillar protein. The results showed that the hydrolysate significantly affected the digestion characteristics of MP. During gastric digestion, the addition of the hydrolysate delayed the exposure of hydrogen bonds in MP, enhanced the surface hydrophobicity and maintained the structure of the protein. With increasing digestion time, the fluorescence intensity and reactive sulfhydryl content of MP gradually decrease.