Gold nanoclusters are attractive because of their electronic and optical properties. Many theoretical models have been proposed to explain their electronic structures through an electron-counting approach. However, subtle features may not be well explained by electron-counting rules. In this work, we have discovered a unique example of ligand-controlled skeletal bonding in two recently reported gold nanoclusters with very similar compositions and geometries. We have shown that the superatomic orbitals of the common kernel of the two clusters undergo different ligand-field splitting because of the different ligand-field strengths in the two clusters. Such a difference is clearly revealed by constructing the Jellium orbitals via an orbital alignment process, and a subsequent localization of the Jellium orbitals allows us to obtain localized bonding models. Finally, on the basis of localized bonding models, we predict the existence of a ligated gold cluster with a [Au-32](4+) kernel.