The unique site substitution of Zn in the structure of tetragonal and atomically ordered Cu6Zn2Sb2, followed by the formation of Cu5Zn3Sb2, has been addressed from fundamental perspectives. First principles energy calculations, and semi‐empirical electronic structure calculations using the density of states, crystal orbital Hamilton population, crystal orbital bond index and Mulliken population analysis were performed to understand the observed substitution pattern and the narrow homogeneity range of the titled compound. Mulliken and Löwdin’s approach of charge analysis explain the experimentally proved ‘coloring’ based on the ‘site energy’ argument. The concept of ‘topological charge stabilization’ has been introduced in this context. Valence electron concentration and the optimization of the partially covalent Cu‐Sb interactions also play pivotal role in the electronic stability of the titled phase.