The three dimensional structure of anti-DON Scfv antibody was modeled and refined using homology modeling and molecular mechanics methods. Procheck and verify_3D methods were used to confirm the models reliability. The recognition and interaction between voitoxin DON and its Scfv antibody were studied via molecular docking method. The result indicated that DON located at the active site of chain VL, binding to VH by several residues in their critical region, and formed a hydrogen bond with residue Pro107. Molecular dynamics simulation and MM/GBSA methods were used to calculate the binding free energy between DON and its Scfv. The calculated binding free energy agreed with experimental index. It was also indicated that the formation of this complex was mainly driven by the hydrophobic interaction. Hydrogen bond analysis and energy decomposition showed that Pro107 was the most important residue which contributed a stable hydrogen bond and strong van der Waals interaction. This research provides some important clues for structure design of anti-DON Scfv antibody, and useful theoretical instruction for the study and development of new types Scfv of toxin-like small molecules.