Abstract: Crown ether could separate the metal ions and their isotopes selectively and efficiently, however, the rapid selection of complex with suitable structure is still a challenging problem. Although the theoretic calculation has been used to study the interaction between metal ions and crown ether ligand, the calculated binding energy is higher than the experimental value. In this study, the coordination of a series of crown ethers (9C3, 12C4, 15C5, 18C6) with metal ions was systematically calculated based on the density functional theory, using dimethoxyethane (DME) as model compound. The metal ions can reduce the energy barrier between DME conformers and the reduction increased with the increase of charge-to-radius ratio of the metal ion. For a metal ion-crown ether complex. The dynamically favored conformer, the thermodynamically most stable conformer and the conformer which has the largest binding energy are in general not the same one. This may be attributed to that the experimental binding energy measured was considerably lower than the calculated binding energy reported in previous studies. The isotope effect of the metal ion-crown ether complexes is mainly determined by the relative mass difference of the different metal isotopes and the coordination bond length, and related with the conformer of crown ether. For same metal ion-crown ether complex，the metal isotope with higher mass has lower free energy, for 7Li and 6Li, the conformer of Li-12C4 with the largest isotope effect was found. In this work, a simple and efficient method to classify the conformers of metal ion-crown ether complexes was developed, which can be used in theoretical calculations for the similar macrocyclic ligands and improve the accuracy of binding energy of complexes. Particularly, this work provides the important fundamental information for the quick screen of structure of crown ether for the selective separation of metal ions and their isotopes.