Characteristics of pyrimidine bases are demonstrated on the crystals of the ternary copper(II) complexes consisting of bpy and pyrimidine-amino acid. Hemiprotonated CH+:C pair is important for the formation of intermolecular triple hydrogen bonding interaction, mimicking i-motif of DNA. The electron-donating effect in thymine ring among pyrimidine bases also promotes intermolecular pi-pi stacking interaction.