Two types of functional monomers, 3-(2-aminoethylamino)-propyl-trimethoxysilane (AAPTS) and 3-aminopropyl-triethoxysilane (APTES), with similar amino groups but different denticity (AAPTS: bi-dentate; APTES: mono-dentate) were used to prepare Cu-ion-imprinted hybrids (IIHs), and their influences on the imprinting quality, adsorption ability, and selectivity of the IIHs were symmetrically investigated. The AAPTS-IIHs exhibited the highest imprinting factor (IF) of 17.7 at the Cu/AAPTS = 1/1 and the highest Cu selectivity (k > 6.5) at the Cu/AAPTS = 0.5–1/1, whereas the two corresponding performances (IF = 22.6, k > 1.7) in the APTES-IIHs occurred at the Cu/APTES molar ratio of 0.124/1 and 0.5/1, respectively. Stronger complexation ability of the bidentate ligand led the AAPTS-IIH to exhibit 6.3–6.9 times higher Cu affinity than the APTES-IIH powder. In addition, it resulted in a higher degree of homogeneity among the binding sites and created more selective environment within the imprinted cavities than the mono-dentate APTES monomer did. Square-planar 4-coordinate and linear 2-coordinate Cu complexes were the major forms imprinted in the AAPTS-based and the APTES-based systems, respectively. The exclusion ability of the AAPTS-IIH for the reference ions was in the order of Pb2+~Zn2+ > Ni2+ > Hg2+, while it was Zn2+> Pb2+> Ni2+> Hg2+ in the APTES-IIH powder. The imprinted hybrids select ions mainly based on the coordinate geometries of the ion-complexes, and the complexation stability was the second priority.