With the view of increasing the understanding to the anti-scaling mechanism in the membrane process, zeta potential on the anti-scalant (Calgon and PAA) modified sub-micro calcite surface was measured and was further characterized with a molecular simulation. Experimental results show that the original positively charged calcite in an aqueous solution is reversed to be negatively charged by introducing anti-scalants at a dosage of ppm level. On the basis of theoretical calculation, the observed reversal is resulted from the statistically predominant orientation of negative potential-determining groups in the adsorbed anti-scalant molecules, i.e. PO and CO, stretching against the calcite surface. A negative zeta potential prevailing on the calcite surface can effectively prevent the calcite from precipitating on the membrane surface. In the presence of anti-scalants, zeta potential on the sub-micro calcite surface is a sensitive function of calcite content, anti-scalant concentration, salt concentration, and pH of the suspension.