Abstract：Acetohydroxyacid synthases（AHAS） which play an important role in biosynthesis of branched chain amino acid, are a group of enzymes widely distributed in plants and microorganism, and it is a popular target of many herbicides. ZJ0777 is a novel herbicide possessing many merits including low toxicity, low residue and high selectivity. The interaction between ZJ0777 and AHAS is studied via molecular docking using discovery studio program. The docking results indicate that ZJ0777 mainly interacts with residue Arg377, Trp574 and Ser653, which is very similar to the binding model of CIE in the crystal structure of AHASCIE complex. CIE has more hydrogen bond interactions with AHAS, and ZJ0777 has more ππ interactions with AHAS. AHASZJ0777 complex obtained by docking and AHASCIE complex are performed 1135 ps molecular dynamics (MD) simulations. RootMeanSquare deviation (RMSD) of the backbone atoms and the inhibitor atoms with respect to starting structure are calculated to estimate the quality and convergence of MD trajectory. The plots of RMSD as a function of simulation time imply that each system has reached stable and equilibrated state, thus it is reasonable to use these simulation data for further analysis. Binding free energy is calculated using MMGBSA method based on the last 200 snapshots of the MD trajectories. The results imply that the formation of the complex is mainly driven by gasphase Vander Walls interaction, gasphase electrostatic interaction and nonpolar solvation interaction. The mechanism of ZJ0777’s high biological activity is elucidated from theoretical perspective, which provides basis for the designing and optimizing of Pyrimidinyloxybenzylamine analogue inhibitors.