Small changes in the terminal region can result in significant differences in protein folding and aggregation for several important proteins. In this work, we described the impact of the C-terminus on determining the assembly process of amylin peptides via Thioflavin T (ThT) fluorescence assay, photo-induced cross-linking of unmodified proteins (PICUP) and conducted SDS PAGE-silver staining experiments. It has been proved that Amylin37-CONH2 aggregated remarkably faster than Amylin37-COOH and there are more LMW oligomers during the aggregation process for Amylin37-COOH. From the molecule dynamics simulation of amylin37-COOH and amylin37-CONH2 dimers, we found that the amylin37-CONH2 dimers are more stable than amylin37-COOH, which may promote the aggregation process. This work provides us new clues to understanding the underlying mechanism of peptide aggregation and the development of toxicity induced by terminal differences and will be helpful for future work involving mutations and modifications at specific residues within these peptides.