Peptide-based fluorescent materials hold promise for applications in energy harvesting and biomedicine. One remaining challenge is to overcome the barrier of fluorescence red shift, especially for peptide probes merely made of natural amino acids. Here we demonstrated an about 100 nm fluorescence red shift using a tripeptide GYK. Under UV illumination or in Fenton reactions, the hydroxyl free radical-based oxidation crosslinks GYK tripeptides into dimers, which can further act as building blocks to hierarchically assemble into nanostructures of different sizes and finally can shift the fluorescence from blue to green color (∼510 nm). Such assemblies can form core-shell-like nanostructures through further crosslinking of their surface with additional GYK monomers, which can not only make the nanostructures more robust but also efficiently improve their quantum yields. This research will deepen our understanding of bioluminescence, which sheds light on various biomedical applications of peptide-based fluorescent probes.