A novel functional hybrid mesoporous composite material (CMP) based on chitosan and MCM-41-PAA was reported and its application as an excellent adsorbent for Hg(II) ions was also investigated. Innovatively, MCM-41-PAA was prepared by using diatomite and polyacrylic acid (PAA) with integrated polymer–silica hybrid frameworks, and then CMP was fabricated by introducing MCM-41-PAA to chitosan using glutaraldehyde as a cross-linking agent. The structure and morphology of CMP were characterized by X-ray diffraction, Fourier transform infrared spectra, thermogravimetric analysis, scanning electron microscopy and Brunauer–Emmett–Teller measurements. The results showed that the CMP possessed multifunctional groups such as –OH, –COOH and –NH2 with large specific surface area. Adsorption behaviour of Hg(II) ions onto CMP was fitted better by the pseudo-second-order kinetic model and the Langmuir model when the initial Hg(II) concentration, pH, adsorption temperature and time were 200 mg l−1, 4, 298 K and 120 min, respectively, as the optimum conditions. The corresponding maximum adsorption capacity could reach 164 mg g−1. According to the thermodynamic parameters determined such as free energy, enthalpy and entropy, the adsorption process of Hg(II) ions was spontaneous endothermic adsorption.