The complexation reactions of ethylenediaminetetraacetate (EDTA(4-)) and S,S-ethylenediaminedisuccinate (S,S-EDDS(4-)) with Co(2+), Ni(2+), Cu(2+), Zn(2+), and Cd(2+) cations are investigated by using the DFT/B3LYP method. The hydration reaction of each metal ion with solvent water cluster is considered with a mixed cluster/continuum model. The subsequent metal complexation is treated as a substitution reaction of the coordinated water molecules by the amino polycarboxylic acid ligand. Thermodynamic cycles are schemed to evaluate the free energy changes for both hydration and complexation processes. The values of complexation free energy changes show that the stabilities of metal complexes with the isomeric ligands follow the order of [M(S,S-EDDS)](2-) in trans(O(6))-conformer < [M(S,S-EDDS)](2-) in trans(O(5))-conformer < [M(EDTA)](2-), implying that the failure to observe the trans(O(6)) conformer under experimental conditions is attributed to its inherent instability. The same trend appears in our steric strain analysis on the various chelate rings in complexes. Because the [M(S,S-EDDS)](2-) in trans(O(6)) complex is not available, we focus on the other two series of complexes with concerned metal ions. The stabilities decrease in the order Cu(2+) > Ni(2+) > Co(2+) > Zn(2+) > Cd(2+) and Cu(2+) > Ni(2+) > Co(2+) > Cd(2+) > Zn(2+) for trans(O(5))-[M(S,S-EDDS)](2-) and [M(EDTA)](2-), respectively. These two tendencies are shown to be consistent with the decrease in the metal-to-ligand charge transfer. Meanwhile, a good quantitative correlation is found between the complexation free energies and the dipole moments for all complexes (excluding the case of Cu(2+)). The far-infrared spectra are present to investigate the characteristics of metal-dependent vibrations, and the further natural bond orbital (NBO) method is taken to show the nature of metal-ligand bonding interactions. Finally, and perhaps most importantly, degrading products of both amino polycarboxylic acids are successfully predicted through calculating the dissociation energies of all C-N bonds in free EDTA, S,S-EDDS, and their successive products. Degradation mechanisms with intramolecular hydrogen transfer are proposed for the biodegradation reactions of S,S-EDDS and its product N-(2-aminoethyl) aspartic acid (AEAA).