The effect of metal ions on the molecular clustering of cytidine in aqueous solution was studied by mass spectrometric analysis of clusters isolated from liquid droplets, and two types of cytidine clustering depending on the coexisting ions were observed. In the presence of alkali metal ion (Li+, Na+, K+) or alkaline earth metal ion (Mg2+, Ca3+) in solution, cytidine molecules aggregated around these ions through the electrostatic interaction, which is similar to the solvation of ions by solvent molecules. In these cases, the predominant cytidine clusters were Mn+(Cy)(a), where a = 1 similar to 4 for alkali metal ion and a = 1 similar to 8 for alkaline earth metal ion, respectively. The number of cytidine molecules in the clusters had strong dependence on the charge density of the metal ion. On the other hand, in the presence of other divalent metal ions (Mn2+, Zn2+) having 3d electrons, the cytidine clusters had a specific structure represented by M2+Cl-(Cy)(b), where b = 2 or 3. This was characterized as coordination of cytidine to the metal ion, where the cytidine works as a bidentate ligand. These showed that the clustering of cytidine was controlled by the interaction with the coexisting metal ion in a solution. This would concern the role of a metal ion on the biological processes.