To reveal the potential fungicidal mechanism of 5-((4-((4-chlorophenoxy)methyl)-5-iodo-1H-1,2,3- triazole-1-yl)methyl)-2-methylpyrimidin-4-amine (PA-1) against Botrytis cinerea (B. cinerea), the three-dimensional structure of B. cinerea pyruvate dehydrogenase complex E1 component (PDHc-E1) is homology modeled, as the PA-1 shows potent E. coli PDHc-E1 and B. cinerea inhibition. Subsequent molecular docking indicates the PA-1 can tightly bind to B. cinerea PDHc-E1. Molecular dynamic simulation and MM-PBSA calculation both demonstrate that two intermolecular interactions, π-π stacking and hydrophobic forces, provide the most contributions to the binding of PA-1 and B. cinerea PDHc-E1. Furthermore, the halogen bonding interaction between the iodine atom in PA-1 and OH in Ser181 is also crucial. The present study provides a valuable attempt to homology model the structure of B. cinerea PDHc-E1 and some key factors for the rational structure optimization of PA-1.