Alkoxysilane-grafted silica/polyhedral oligomeric silsesquioxane with methacryl substituents (SiO2/silane/POSS) hybrid material was synthesized according to hydrolyzation and condensation reactions in the so-called “bifunctionalization process.” It is a new attractive system because of its physicochemical, especially thermal and structural, properties. This innovative method of preparation as well as specific physicochemical and useful properties determine the potential applications of such products in many industries. The structure and physicochemical parameters of obtained hybrid systems were characterized using infrared spectroscopy (FTIR),13C and29Si solid-state nuclear magnetic resonance (CP MAS NMR), and thermal analysis. The mechanism of bifunctionalization reaction was proposed. The chemical immobilization of silane coupling agent and Methacryl POSS onto silica support surface was noted during the study. Those changes caused a significant increase in the hydrophobic character of fillers obtained. Moreover, changes in thermal stability of SiO2/silane/POSS hybrid systems in comparison to pure POSS modifier were also observed.