We performed this study in order to investigate the effect of ultrasound (US) and ultra-high pressure (UHP) treatments on the flavor-binding capacity of proteins from the perspective of its structural alteration. Hexanal, 1-octen-3-ol, or 3-methylbutyraldehyde was added to myofibrillar protein (MP) extracted from topmouth bleak (Culter alburnus) before being treated by US (200 and 300 W) or UHP (100 and 250 MPa) for 15 min. After the treatments, the changes in volatile compound concentrations were measured to verify the effect of protein structural alteration on its flavor-binding capacity. The results showed that different treatments affected the binding capacity of fish MP to flavor substances. Both US and UHP treatments substantially increased the hexanal-binding capacity of MP, but slightly decreased the 3-methylbutyraldehyde-binding capacity of MP, and decreased the 1-octen-3-ol-binding capacity of MP to 24%-35%. Among all the treatments tested, UHP treatment at 100 MPa had the greatest effect on the flavor-binding capacity of MP. Both treatments affected the free and total sulfhydryl content and surface hydrophobicity of MP, and increased the maximum fluorescence intensity and ultraviolet (UV) absorption intensity, with the increase being more pronounced upon addition of volatile compounds. In conclusion, US and UHP treatments can effectively change MP structure, thereby being conducive to the flavor-binding ability of fish.