Abstract: The behavior of 1-(4-Methylpyrimidine-2-yl)-3-(2-nitrobenesulfonyl)urea (I) in aqueous solution was studied by means of molecular dynamics simulation method. The structure activity relationship of the molecule of this new ultra-low dosage and environmental benign herbicide was discussed: while in aqueous solution, its molecule has both stretching and curling conformation while in non-polar as CCl4 solvent, it has stretching conformation. The internal rotation energy barrier in aqueous solution of (I) was calculated to be 20.6 kJ/mol, which indicated of conformations of (I) in aqueous solution could be inter changeable.