Polymorphic structure of polyhedral oligomeric silsesquioxanes (POSS) derived from hydrolytic condensation of vinyltrimethoxysilane was validated by the spectral characterization, such as FTIR, UV-MALDI-TOF MS, etc. Discover module of Materials Stutio (MS) software which is a molecular dynamic simulations (MDS) program has been used to estimate the self-diffusion coefficients of small gas molecules in models of hybrid materials that validates the corresponding anticorrosion-experiment results. The models of 3D-amorphous cubic unit cells of different numbers of Si atom and hydroxyls generated during the hydrolytic condensation (T6, T7, T8, T9, T10, T8(OH)2 and T8(OH)4 cells), were employed to investigate self-diffusion coefficients by MDS for the N2, O2, Cl2, CO2, NO2, SO2 and H2O molecules. The simulations results showed that all seven self-diffusion coefficients of N2, O2, Cl2, CO2, NO2, SO2 and H2O in cells increased with the numbers of Si atoms and the generated hydroxyls. This increasing was discussed by the calculation, compared to the vinyltrimethoxysilane hybrid systems.