Calcite is a common scale in water cooling systems treated and controlled with Organic phosphonates. The effect of three phosphonic acids (ethylene diamine tetra(methylene phosphonic acd), EDTMP; hexamethylene diamine tetra(methylene phosphonic acd), HDTMP; and diethylene triamine penta(methylene phosphonic acd), DTPMP) on the growth of the calcite has been investigated by pH curve method(pHCM). Experimental data obtains by pH value measurement of Ca(HCO3)2 supersaturated solution before and after precipitation. Besides, molecular dynamic simulations of the interaction of the phosphonic acids with the calcite(104) indicate the inhibitor effectiveness: EDTMP< DTPMP< HDTMP according to the difference in the carbon chain between nitrogen atoms. This is in agreement with the pHCM measurements.