The molecular dynamics modeling method is used to study the adsorption characteristics of 1-hydroxyethyldene-1,1-diphosphonic acid(HEDP) on the {104} surface of calcite. The simulated 3-D molecular graphs display that the oxygen atoms in the phosphonate groups of HEDP are strongly electro negative and have high affinity to cationic regions of the surface of the crystals, which results in the inhibitor molecular binding to the crystal surface to form the “multi-site stereo matching". The calculated results show that the adsorption energy of HEDP on the surface, step and kink are -5.2eV,-7.0eV and -23.5eV, respectively. It suggestes that HEDP malecules prefer to adsorb on the kinks to inhibit the development of steps on the calcite surface.