In recent years, new deposits of polymineral complexes have been actively discovered and are beginning to be developed in the Orenburg region of Russia. Knowledge of the structural features of such heterogeneous systems will help provide a controlled structural evolution. Such studies will help shorten the time needed for the introduction of raw materials into production processes of functional ceramics. A selection of physical and chemical methods has been chosen to analyze natural polymineral complexes in order to understand the temperature evolution of their phase composition and structural transformations. The polymineral complexes from deposits in the Orenburg region of Russia are known to be fusible. Infrared spectroscopy and diffractometry methods have been used to identify six to ten crystalline phases in the studied objects. The main phases have been identified as follows: quartz, calcite, kaolinite, montmorillonite, clinochlore, and magnetite. Structural changes were induced by heating the sample to 1200 K at a rate of 10 K/min while recording derivatograms. EPR spectroscopy established that impurity centers have an ambiguous role in the evolution of natural mineral structures. They can both stabilize crystal lattices and cause distortions due to the Jahn-Teller effect. This is particularly true for layered lattices that contain octahedral motifs with a central impurity ion. It has been demonstrated that impurity centers Fe3+ and Mn2+ act as spin labels for structural transformations. As a result of the destruction of crystal components, these impurity centers form clusters with each other and become undetectable by other methods of analysis.