The inclusion of Ge in hexagonal B35 type CoSn leads to the formation of a new ternary substituted ordered variant Co3Ge2Sn. The experimentally reported crystallographic site‐occupancy pattern of this compound has been fundamentally addressed by the PBE‐GGA density functional theory‐based Mulliken population analysis. The site preference of Ge in the structure of Co3Ge2Sn is governed by the rule of ‘topological charge stabilization’. It turns out that the covalent inter‐layer heteroatomic Co−Ge bonds play a profound impact on the formation and stability of the compound. The structure of Co3Ge2Sn is decided by a combined factor of site energy and bond energy.