A novel impedimetric sensor, based on DNA intercalator, GR-5 DNAzyme and the low-cost gold interdigitated electrodes (GID), was studied to detect lead ions in this paper. It takes GR-5 DNAzyme as the recognition element immobilized on GID and anthraquinone-2-sulfonic acid (AQMS) as the DNA intercalator for improving its sensitivity of lead ions detection. When the GID modified with GR-5 DNAzyme were incubated in intercalator solution, AQMS will intercalate into the base-pairing regions of GR-5 DNAzyme. In the presence of Pb2+ ions, the GR-5 DNAzyme was activated and the substrate strand was cleaved into two parts at the RNA site (rA), which results in the releasing of AQMS from the GR-5 DNAzyme. With the decrease of AQMS, the magnitudes of the impedance increased, which relates to the Pb2+ concentration, was obtained. Our results demonstrate that the proposed sensor has a detection limit of 0.33 nM, and the linear range from 1 nM to 100 nM with a high selectivity. Finally, the sensor shows an average recovery of 99.31-107.85% when it was used to detect Pb2+ in water samples. Additionally, the GID were made on printed circuit board (PCB) which was cost-effective and mass production because of the mature produce technology. Furthermore, the application of AQMS leads to significantly decrease of the detection limit of the Pb2+. Therefore, the strategy shown that a promising applications in environmental and food-field monitoring.