Water pollution resulting from Hg(II) ions has garnered significant global concern for public health. The flexibility and simplicity of design, cost savings, and ease of operation with adaptive designs provide adsorption with a considerable advantage over other processes. However, MoS 2 is hydrophobic in nature, which limits its efficiency in the removal of Hg(II) ions from water. Therefore, the incorporation of hydrophilic SBA-15 as supporting material, combined with a nanoflower-like layered MoS 2 and its highly reactive exposed edges, produces hydrophilic properties that effectively eliminate Hg(II) from water . A mercury-ion-imprinted polymer (Hg(II)-IIP) was synthesized on the MoS 2 /SBA-15 surface using N-allylthiourea (ATU) as a functional monomer to enhance material selectivity and create dual recognition sites. Characterization investigation using scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared (FTIR), X-ray photoelectron spectroscopy (XPS), and water contact angle showed the successful synthesis of Hg(II)-IIP, excellent hydrophilicity, and close interaction between MoS 2 and SBA-15. The maximum adsorption capacity of Hg(II)-IIP for Hg(II) under optimized adsorption conditions was 567.78 mg•g −1 in 90 min, which was 6 times greater than that of the IIP solely based only on SBA-15, and followed by pseudo-second-order and aligned more closely fits with the Langmuir adsorption isotherm. Furthermore, the adsorption capacity of the synthesized Hg(II)-IIP was greater than that of three other common monomers IIP. Hg(II)-IIP possesses a strong ability to regenerate, while also showing better selectivity for Hg(II) in the presence of other interfering ions, indicating its robust anti-interference capability in the multivariate mixed solution. The analysis of the actual sample indicated that Hg(II)-IIP attained recoveries between 97.92 and 100.28% in water samples. Theoretical calculations using density functional theory (DFT) and frontier molecular orbital (FMO) indicated that the binding energy of the sulfur atom forming a tetra-ligand with Hg(II) on ATU was 0.6511 eV greater than that of a diligand. The energy gap was determined to be 0.1550 eV, supporting the preference for S−Hg tetra-ligand adsorption.