The results of studying the energy spectrum of electrons and holes localized in second-type Ge/Si heterostructures with Ge quantum dots are presented. In such structures, holes are localized at Ge quantum dots, and electrons, in three-dimensional quantum wells, which form in Si at the Ge—Si interface because of inhomogeneous deformations that appear as a result of the difference between the Ge and Si lattice constants. It is shown that changes in the deformations in the assembly of quantum dots as a result of a variation in their spatial arrangement significantly changes the binding energy of electrons, the position of their localization at quantum dots, the binding energy and wave-function symmetry of holes at double quantum dots (artificial molecules), and the exchange interaction of electrons and holes in the exciton composition. A practically important result of the presented data is the development of approaches to increase the luminescence quantum efficiency and the absorption coefficient in assemblies of quantum dots.