A cost-effective adsorbent for highly efficient removal of mercuric Hg(II) ions from aqueous media remains a great challenge. Herein, a novel polymer-based adsorbent of hyperbranched polyethylenimine functionalized carboxymethyl chitosan semi-interpenetrating network composite (HPFC) was fabricated through a facile one-step crosslinking reaction. Notably, the as-prepared adsorbent demonstrated ultra-high adsorption capacity toward the removal of Hg(II) ions. Upon treatment with 20 mg-dosage of HPFC in an aqueous medium (20 mL), the concentration of Hg(II) is decreased from 798.1 mg/L to 0.02 mg/L, which is below the national drainage standard of 0.05 mg/L for industrial wastewater in China. A kinetic study shows that the adsorption of Hg(II) ions follows the pseudo-second-order model, indicating chemical adsorption between Hg(II) ions and HPFC. The maximum adsorption capacity is 1594 mg/g, which is higher than that of many other currently known natural polymer-based adsorbent. Furthermore, this adsorbent exhibits excellent selectivity for removing Hg(II) ions, and the selectivity coefficient to Hg(II) ions is 3-4 orders of magnitude higher than that to Cu(II) ions, Cd(II) ions and Pb(II) ions, respectively. Based on the measurements of Fourier transform infrared spectrum (FTIR) and X-ray photoelectron spectroscopy (XPS) and the density functional theory (DFT) calculations, the adsorption mechanism was proposed. The removal of Hg(II) ions by HPFC is mainly controlled by the interaction between Hg(II) ions and nitrogen functional groups (i.e., amine and imine groups). Significantly, HPFC has superior reusability and could be easily regenerated and reused multiple times. The developed HPFC adsorbent holds high potential in remediating water polluted with Hg(II) ions.