Molecular dynamics simulation and Density Functional Theory were used to investigate the adsorption of two kinds of anti-scalant, ethane diphosphonic acid (EDPA) and polyether polyamino methylene phosphonate (PAPEMP), on the calcite (104) Surface in order to increase the level of understanding of the anti-scaling mechanism in membrane processes for water desalination. Calculation results show that the performance of an anti-scalant is mainly determined by the negative electrostatic potential presented on the anti-scalant modified scale surface. A negative electrostatic potential on the scale surface can prevent not only the agglomeration of scale nuclei in the concentrate but also the precipitation of scale nuclei on the membrane surface. Phosphonate groups in 1,1-EDPA are bifunctional since they simultaneously satisfy the requirements for the electrostatic potential distribution and for the adsorption stability on the scale surface. As concerns PAPEMP, the above requirements are fulfilled respectively by different functional groups, i.e. ether groups and phosphonate groups. To simplify the role of functional groups in the anti-scaling mechanism means that the performance of an anti-scalant can be optimized by the combination of specific functional groups; furthermore, these functional groups can also be adjusted with respect to different scale surfaces.