The formation of complex surface morphology of a multilayer structure, the processes of which are based on quantum phenomena, is a promising domain of the research. A hierarchy of pore of various sizes was determined in the initial sample of porous silicon by the atomic force microscopy. After film deposition by spray pyrolysis, ZnO nanoclusters regularly distributed over the sample surface were formed. Using the electron paramagnetic resonance (EPR) method it was determined that the localization of paramagnetic centers occurs more efficiently as a result of the ZnO deposition. An increase in the number of deposited layers, leads to a decrease in the paramagnetic center relaxation time, which is probably connected with the formation of ZnO nanocrystals with energetically stable properties. The nucleation and formation of nanocrystals is associated with the interaction of particles with an uncompensated charge. There is no single approach to determine the mechanism of this process. By the EPR method supplemented with the signal cyclic saturation, spectral manifestations from individual centers were effectively separated. Based on electron paramagnetic resonance and photoluminescence studies it was revealed that the main transitions between energy levels are due to oxygen vacancies and excitons.