The field of cocrystalline nanoclusters stabilized by thiolates is in a period of rapid development. However, the types of cocrystallization have been limited to a few reported until now, so it is of great importance to investigate and understand the novel cocrystallographic structures. Herein, we design and synthesize a new type of cocrystallization, [Ag23Au2(2-EBT)18Ag22Au3(2-EBT)18]2-[2(PPh4)]2+, characterized by thermogravimetric analysis, X-ray photoelectron spectroscopy, and single-crystal X-ray crystallography. Interestingly, both of the cocrystallized nanoclusters show the same outer-shell geometric structure but diffenent cores (Ag11Au2 vs Ag10Au3). The cocrystal lattice exhibits a multilayer structure in which both of the cocrystallized nanoclusters and the counterion assemble in a layer-by-layer model. Meanwhile, the counterion is found to be critical for formation and stabilization of the target cocrystal. In addition, the target cocrystal shows high thermal stability, and this result possibly originates from the electrostatic and weak interactions in the cocrystals.