The electronic structure of heterometallic cubane-type clusters with core {Mo 3 S 4 M′} (M′ = Cu + , Ni 0 , Pd 0 ) was investigated by the Atoms in Molecules and Electron Localization Function topological methods as well as Energy Decomposition Analysis. It was found that {Mo 3 S 4 Cu} and {Mo 3 S 4 M′} (M′= Ni, Pd) clusters have a different interaction between molybdenum and heterometallic atoms. In case of the complexes with Ni/Pd atom, the disynaptic basins on the Mo–M′ bonds were observed in contrast to the Cu containing complex. The complex formation between heterometallic fragments and trinuclear molybdenum complex {Mo 3 S 4 } were found to be hindered due to steric interactions. Nevertheless, the formation of the heterometallic cubane-type clusters occurs due to the multicenter and pair covalent interactions between Mo and M′ atoms.