Reactive combinations of aliphatic epoxy resins and functional polysiloxanes form a class of hybrid thermosetting materials with properties that may come from both the organic and the inorganic phases. The two typically immiscible phases form a suspension whose morphology, composition, and thermal properties vary with curing time. The aim of this research was to elucidate the mechanism by which morphology changed with time and to simulate it through Metropolis-Monte Carlo. The selected system was hydrogenated epoxy (HDGEBA) and a synthetic polyaminosiloxane (PAMS). It was studied by DSC, FTnIR, gel point, viscometry, and in-situ laser scanning confocal microscopy. A mechanism for morphology generation was proposed and simulated, exploring a wide range of values of the “a priori” relevant variables. The essential features were captured by simulations with a reasonable agreement with experimental data. However, the complete process was more complex than the geometrical approach of the simulation. The main deviations that were found and qualitatively explained are: (i) the induction period on the rate of coalescence, and (ii) PAMS-rich domain average size increases faster than predictions.