The chitosan-poly(vinyl alcohol) (CTS-PVA) hydrogel with three-dimensional network structure was developed via a glutaraldehyde cross-linking method in combination with an alternate freeze-thawed process. The formation of the three-dimensional network structure was confirmed by SEM and parallel FT-IR measurements. According to the analysis of parallel FT-IR measurements and MM+ molecular mechanics theoretical simulation, the three-dimensional network architecture is built mainly by inter- and intra-molecular hydrogen bonds as well as C=N bonds formed by the reaction of -NH2 groups of CTS and -CHO groups of glutaraldehyde. Parallel adsorption experiments and comparative studies showed that the hydrogel adsorbent has superior adsorption capacity and selectivity for Hg(II) ions. Its adsorption capacity for Hg(II) ions reaches 585.90 mg/g. Its selectivity coefficient of the hydrogel for Hg(II) ions is 487.7, 36642.5, 284298.5 times higher than that for Cu(II) ions, Pb(II) ions, and Cd(II) ions, respectively. Its selective adsorption mechanism for Hg(II) ions was proposed based on FT-IR and XPS spectral analysis before and after Hg(II) adsorption. All nitrogen-containing functional groups are involved in Hg(II) adsorption, especially, -NHCOCH3 and C=N groups are the main selective functional groups responsible for Hg(II) adsorption. The existing form of the adsorbed Hg(II) may be in mercury acetate.