Transition metal-containing ionic liquids (TM-ILs) have attracted a great deal of attention in recent years, due to their unique physical and chemical properties. In this work, several representative TM-ILs, such as the cations consisting of silver(I) center coodinated by two n-alkylimidazole ligands ([(C(n)im)Ag-(mim)](+)) and the anions involving mercury(II) (HgCl3-), zinc(II) (ZnCl3-), and rhenium(VII) (ReO4-), were investigated using density functional theory calculations. First, the structural and energetic properties of the ion pairs for these TM-ILs have been examined in detail and compared with properties for conventional ILs. It was found that the interactions between the cations and anions, including hydrogen bonds and electrostatic interactions, in TM-ILs become weaker in strength than those in traditional ILs. In particular, the calculated geometric and energetic features compare fairly well with the experimental results, such as melting points and X-ray crystal structures of these TM-ILs. Then, the structures and energetics of ion-pair dimers for three ILs containing HgCl3-, ZnCl3-, and ReO4- were also explored, to gain a deeper understanding of the properties of TM-ILs. Finally, a survey of the Cambridge Structural Database (CSD) was undertaken to provide some crystallographic implications of TM-ILs.