A new strategy on the understanding of selective and sensitive identification of Pb(II) using combined experimental and theoretical efforts is described. Amorphous phase formation of exfoliated nano-zirconium phosphate (ZrP) has been prepared via a hydrothermal process and subsequent intercalation reaction. Exfoliated ZrP was used as coating on the electrode surface, and it was found to be selective and sensitive for Pb(II) detection due to its selective adsorption ability. To better and scientifically understand the microscopic adsorption mechanism, density functional theory (DFT) calculations about the details of chemical interactions between heavy metal ions and exfoliated ZrP were carried out at an atomistic level. It is verified that the exfoliated ZrP shows the strongest adsorption capability toward Pb(II) among all heavy metal ions, thereby resulting in selective detection consequently. With our combined experimental and theoretical efforts, we are able to provide a new route to realize the improved selectivity in electrochemical sensing of toxic metal ions.