Abstract Changes in the structure of phyllosilicate microparticles of submicron fractions of polymineral clay with an average size of 290 nm, as well as changes in the positions of impurity ions of transition metals in the crystal lattice, were studied by X-ray diffraction analysis, Fourier transform infrared spectroscopy, and high-resolution electron paramagnetic resonance spectroscopy. The main composition of microparticles included clinochlore, montmorillonite, calcite, and quartz. Structural transformations were stimulated by heating the samples to 1200 K at a rate of 10 K/min. A decrease in the number of crystal structures of microparticles was recorded due to the amorphization of montmorillonite, the decomposition of calcite, and the formation of sillimanite. Structural rearrangements of crystal cells containing impurity paramagnetic ions Fe3+ and Mn2+ in submicron particles of clinochlore and montmorillonite, accompanied by displacements and changes in the chemical bonds of these ions, were recorded by the ion-electron paramagnetic resonance method. It is shown that when microparticles were heated to 1200 K, the impurity paramagnetic ions of transition metals did not go beyond their crystal cells.