The uptake mechanism of heavy metal ions in layered double hydroxides (LDHs) is investigated in this paper via solid-solution exchange experiments and first principle study. The uptake capacities of C-LDHs for heavy metal ions from solutions are experimentally investigated and the structures of LDHs doped with various heavy metal ions are revealed. The doped structures of LDHs are further re-established with first principle calculations. The results show that Cu²⁺ or Cr³⁺ ions are immobilized in the form of isomorphic substitution for Mg²⁺ and Al³⁺ in the plate of the layered structure, respectively, during reconstruction of calcined LDHs, forming a non-stoichiometric structure. The structure of the Cu²⁺ doped LDHs is identified as [Mg²⁺ _{(1−x)(1−z)}Cu²⁺ _(1−x)zAl³⁺ _x(OH)₂] Aⁿ⁻ _x/n·yH₂O, where z is the molar ratio of Cu²⁺ to Mg²⁺. The structure of Cr³⁺ doped LDHs is identified as [Mg²⁺ _1−x Cr³⁺ _xzAl³⁺ _x(1−z)(OH)₂] Aⁿ⁻ _(x+z)/n·yH₂O, where z is the molar ratio of Cr³⁺ to Al³⁺. The Cu²⁺ or Cr³⁺ ions in the hardened cement paste modified with calcined Mg-Al LDHs as immobilizing admixture can be efficiently removed from the pore solution and chemically stabilized in the structure of LDHs.