The complexes of doubly charged cations, [CuLn]2+, [CuL(MeOH)n]2+ and single charged cations, [Cu(L–H)Ln]+, [L+H]+, [L2+H]+, and [B+H]+, etc. (L = cytidine, B = cytosine) were observed via electrospray of water and methanol solutions of Cu(NO3)2 and cytidine. The peak distribution for [CuLn]2+ shows that the [CuL2]2+ and [CuL4]2+ are the highest peaks, then followed by [CuL3]2+, [CuL5]2+, etc.Collision-induced dissociation (CID) of [Cu(L–H)Ln]+(n = 0,1), [CuLn]2+(n = 2–6) and [CuL(MeOH)n]2+(n = 1, 2) was investigated using the ESI-MS/MS instrument, and the structure and thermal energy for the most of these complexes were also calculated with ab initio and DFT methods through Gaussian 09 program. For [Cu(L–H)L0-1]+, the primary dissociation only involved a ribose group, including ribose group lost, ribose side chain and ribose ring broken. The calculation result shows that the deprotonated site for [Cu(L–H)]+ is the N-atom in the amino group of the cytidine base. The inter-ligand proton transfer was observed to dominate the CID of all doubly charged CuII–cytidine complexes, [CuLn]2+ (n = 2–6), and other channels, including charge reduction dissociation, lost neutral ligands were also observed. The protonated cytidine dimer, [L2+H]+, produced in the CID of [CuLn]2+ (n = 4–6), can further break into [L+ H]+ and neutral L, and the structure is proposed to be from the interaction of two cytidinesviahydrogen bonds. The protonated trimeric cytidine was also observed in the dissociation of [CuL6]2+. Three charge reduction dissociation channels were observed in the CID of [CuL(MeOH)]2+. Unlike the CuII–guanosine complex, the radical cation [CuLn]+ was not observed in the CID process of the [CuLn]2+, and the reasons are attributed to the higher ionization energy and proton affinity, which makes the inter-ligand proton transfer more favorable than the electron transfer from ligand to Cu2+.