The interaction between herring antifreeze protein (hAFP) and ice crystals was studied by molecular dynamics simulation in this paper. On this basis, the effect of hAFP on the quality attributes of largemouth bass after three freezing-thawing (F-T) cycles was studied. Scanning electron microscope was conducted to analyze the microstructure changes of muscle fibers. The content of dityrosine/total sulfhydryl/carbonyl and the Ca2+-ATPase activity were measured to explore the degree of protein oxidation. Raman and intrinsic fluorescence spectra were used to measure the protein secondary structure and tertiary conformation. Results showed that hAFP protected the organisms from freezing by binding to the ice crystals, decreasing the freezing point and inhibiting the recrystallization. Furthermore, hAFP combined with chitosan magnetic ([email protected]3O4) nanoparticles or vacuum impregnation hAFP was shown to be an effective method to reduce the mechanical damage of ice crystals to samples, and decrease the oxidation degree of samples during F-T cycles.