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Quenched Ge–Sb–Te (GST) compounds exhibit strongly disordered metastable structures whose average structure corresponds to a distorted rocksalt type with trigonal symmetry. Depending on the composition and thermal treatment, the metrics remain more or less pseudocubic. The corresponding stable phases show regular sequences of distorted rocksalt-type blocks that formally result from layer-like cation defect ordering. These thermodynamically stable layered phases can gradually be approached by annealing the metastable (pseudo)cubic compounds that are accessible by quenching high-temperature phases. The relaxation of Te atoms in the vicinity of the defect layers leads to van der Waals gaps rather than defect layers in an undistorted matrix. The partially ordered phases obtained show defect layers with an average distance and arrangement depending on the composition and the thermal treatment of the samples. This variation of the nanostructure influences the lattice thermal conductivity (κL) and thus the thermoelectric figure of merit (ZT). This results in ZT values up to 1.3 at 450 °C for bulk samples of Sb2Te3(GeTe)n (n = 12 and 19). The stability ranges of the various phases have been examined by temperature programmed X-ray powder diffraction and can be understood in conjunction with the changes of the nanostructure involved. The real structure of phases Sb2Te3(GeTe)n (n = 3–19) has been investigated by high-resolution electron microscopy (HRTEM) and scanning transmission electron microscopy (STEM)-high-angle annular dark-field (HAADF) with respect to the stoichiometry and synthesis conditions. The correlation of the nanostructure with the thermoelectric properties opens an interesting perspective for tuning thermoelectric properties.