Generally, anthocyanin is extremely vulnerable when exposed to oxidants, alkaline, heat, and metallic ions in the ambient environment. In this research, we use an amphiphilic peptide of eighteen amino acids, named C6M1, to encapsulate anthocyanin by co-assembly mechanism. The representative size of anthocyanin-encapsulated peptide nanocomposites is less than 100 nm, with a high encapsulation efficiency of 77.06% and a maximum mass loading capability over 600 wt % (w/w). Particularly, we find that the co-assembly with anthocyanin causes a conformational change of the C6M1 peptide, switching from α-helical structure to β-sheet dominating structure, thus realizing the encapsulation of anthocyanin. The intermolecular interaction between C6M1 peptide and anthocyanin is further characterized via fluorescence quenching experiments. Moreover, stability enhancement of anthocyanin and physicochemical properties of the C6M1-anthocyanin nanocomposites are investigated quantitatively. Briefly, our results show that the C6M1 peptide greatly improves the tolerance of anthocyanin to increase of pH, metallic ions, and hot temperature; and maintains the intrinsic capacity of anthocyanin of scavenging free radicals. • An amphiphilic peptide encapsulates anthocyanin with a high mass loading. • Secondary structure of peptide is converted from α-helix to β-sheet during the encapsulation. • Molecular interactions are found between peptide and anthocyanin via fluorescence spectrum. • Stability enhancement of peptide-anthocyanin against pH, metallic ions, and temperature.