The stepwise hydration effect on the glutamic acid–Ca²⁺ (GC) complexes in the gas phase has been investigated by density functional theory (DFT) calculations. The thermodynamics parameters for the hydration reactions, the stepwise hydration energies and accurate geometries have been explored. To elucidate the Ca²⁺–ligand interaction, the charge transfer, bonding analysis and IR spectroscopic characteristics have also been investigated. The correlating data have shown that all of the stepwise hydration reactions are enthalpy-driven because of the relatively small value of ΔS, but the number of coordinated water molecules in the first shell of Ca²⁺ is not limitless. In our study, the optimal coordination number (CN) of Ca²⁺ in the first shell is 6 or 7; the former value agrees well with the data reported in the Protein Data Bank (PDB), and the latter is the reflection of the most frequent Ca²⁺-binding motif, EF-hand, in soluble proteins. Furthermore, the self-consistent reaction field (SCRF) and higher-level MP2 calculations have confirmed our conclusions. Additionally and very importantly, the stepwise hydration in either the first or second coordination shell can weaken the glutamic acid–Ca²⁺ interaction gradually till the glutamic acid ligand is replaced by the added water molecules, resulting in the conversion of coordination mode of the glutamic acid to Ca²⁺ from the inner-sphere one to a peripheral interaction mode, just like the ligand exchange process in the Ca²⁺ release channel existing in the real biological system. Finally, the similarities and discrepancies between our model and the Ca²⁺-channel in vivo have been compared.