Polypyrrole/carbonaceous nanospheres (PPy/CNSs) were synthesized for the first time and exactly employed in the selective detection for Hg(II) and Pb(II) on the modified screen-printed electrode under ultra-low concentration. The method is based on the selective adsorption of PPy/CNSs toward heavy metal ions. With both of the advantages of CNSs and PPy in electrochemical detecting, excellent sensitivity (0.113μAnM−1 for Hg(II) and 0.501μAnM−1 for Pb(II)) was achieved. Meanwhile, the detection limits achieved (0.0041nM for Pb(II) and 0.0214nM for Hg(II), 3σ method) are much lower than the guideline values in drinking water given by the World Health Organization. The analytical application of the present electrode toward the detection of metal ions in a real sample has also been successfully demonstrated.