Mg29-xPt4+y represents the family of complex intermetallic compounds (complex metallic alloys, CMAs). It crystallizes in the cubic non-centrosymmetric space group F4̅3m with a = 20.1068(2) Å and around 400 atoms in a predominantly ordered arrangement. The local disorder around the unit cell origin is experimentally resolved by single-crystal X-ray diffraction in combination with atomic-resolution transmission electron microscopy (TEM, high-angle dark-field scanning TEM) studies. The quantum theory of atoms in molecules-based analysis of atomic charges shows that the unusual mixed Mg/Pt site occupation around the origin results from local charge equilibration in this region of the crystal structure. Chemical bonding analysis reveals for Mg29-xPt4+y─rather unexpected for a crystal structure of this size─space-separated regions of hetero- and homoatomic bonds involving three to six partners (bonding inhomogeneity). Pt-containing 11- and 13-atomic units formed by heteroatomic 3a-, 4a-, and 5a-bonds are condensed via edges and faces to large super-tetrahedrons, which are interlinked by Mg-only 6a-bonds. Spatial separation of the regions with different bonding features is the key difference between the title compound and other CMAs, which are characterized by a predominantly homogeneous distribution of heteroatomic bonds.