In this study, a nanocomposite consisting of three-dimensional reduced graphene oxide (3D-rGO) and plasma-polymerized propargylamine (3D-rGO@PpPG) was prepared and used as a highly sensitive and selective DNA sensor for detecting Hg2+. Given the high density of amino groups in the resultant 3D-rGO@PpPG nanocomposite, thymine-rich and Hg2+-targeted DNA was preferentially immobilized on the fabricated sensor surface via the strong electrostatic interaction between DNA strands and the amino-functionalized nanocomposites, followed by detecting Hg2+ through T-Hg2+-T coordination chemistry between DNA and Hg2+. The results of electrochemical measurements revealed that the anchored amount of DNA strands anchored on the 3D-rGO@PpPG nanofilm surface affects the determination of Hg2+ in aqueous solution. It showed high sensitivity and selectivity toward Hg2+ within concentrations ranging from 0.1 to 200 nM and displayed a low detection limit of 0.02 nM. The new strategy proposed also provides high selectivity of Hg2+ against other interfering metal ions, good stability, and repeatability. The excellent applicability of the developed sensor confirms the potential use of plasma-modified nanofilms for the detection of heavy metal ions in real environmental samples and water.