III-nitride heterostructures in the form of multilayered quantum wells (MQWs) or quantum dots (QDs) and interacting Ge QDs (“quantum molecules”) are promising candidates for high-speed intersubband (ISB) optical devices relying on the quantum confinement of electrons. Microstructural parameters (interatomic distances, coordination numbers, and Debye-Waller factors) were determined by means of EXAFS spectroscopy based on the Synchrotron Radiation, and the relationship between the variations in these parameters and the morphology of superlattices and symmetric assembles of QDs were established. The EXAFS technique has been used to study the local structure of thin hexagonal GaN/AlN MQWs grown by ammonia MBE at different temperatures. It is shown that the heterointerface intermixing leads to a decrease in the Ga-Al interatomic distance and the Ga-Ga coordination number in MQWs. The degree of intermixing in the boundary layers rises from 30% to 40% with increase of the growth temperature from 795 to 895 °C. It was found that in the first phase of quantum molecules growth Ge atoms concentration is 25%. With further growth (deposition of the base layers) Ge concentration increases up to 35-45%, depending on the temperature (from 610 to 550 °C) of deposition.