A series of all-thiol stabilized bimetallic Au-Cu nanoclusters, [Au12+nCu32(SR)(30+n)](4-) (n = 0, 2, 4, 6 and SR = SPhCF3), are successfully synthesized and characterized by X-ray single-crystal analysis and density functional theory (DFT) calculations. Each cluster consists of a Keplerate two-shell Au-12@Cu-20 core protected by (6 - n) units of Cu-2(SR)(5) and n units of Cu2Au(SR)(6) (n = 0, 2, 4, 6) motifs on its surface. The size and structural evolution of the clusters is atomically controlled by the Au precursors and countercations used in the syntheses. The clusters exhibit similar optical absorption properties that are not dependent on the number of surface Cu2Au(SR)(6) units. Although DFT suggests an electronic structure with an 18-electron superatom shell closure, the clusters display different thermal stabilities. [Au12+nCu32(SR)(30+n)](4-) clusters with n = 0 and 2 are more stable than those with n = 4 and 6. Moreover, an oxidation product of the clusters, [Au13Cu12(SR)(20)](4-), is structurally identified to gain insight into how the clusters are oxidized.