VX is a highly toxic organophosphorus nerve agent that the Chemical Weapons Convention classifies as a Schedule 1. In our previous study, we developed a method for detecting organophosphorus compounds using peptide self-assembly. Nevertheless, the self-assembly mechanisms of peptides that bind organophosphorus and the roles of each peptide residue remain elusive, restricting the design and application of peptide materials. Here, we use a multi-scale computational combined with experimental approach to illustrate the self-assembly mechanism of peptide-bound VX and the roles played by residues in different peptide sequences. We calculated that the self-assembly of peptides was accelerated after adding VX, and the final size of assembled nanofibers was larger than the original one, aligning with experimental findings. The atomic scale details offered by our approach enabled us to clarify the connection between the peptide sequences and nanostructures formation, as well as the contribution of various residues in binding VX and assembly process. Our investigation revealed a tight correlation between the number of Tyrosine residues and morphology of the assembly. These results indicate a self-assembly mechanism of peptide and VX, which can be used to design functional peptides for binding and hydrolyzing other organophosphorus nerve agents for detoxification and biomedical applications.