Computer simulation has been widely applied in many research fields owing to its superiority in revealing an insight understanding of the phenomena. In this work, molecular simulation method is adopted to model and investigate the gas solubility in polysiloxane materials, aiming to the polymer scientific field. The simulation results calculated by Material Studio 4.0 software show that the proper repeat unit numbers differed with various gas molecule sizes for obtaining accurate calculated solubility, and are correlated to the polarity and volume of branch substitute group. The gyration radii of the target gas molecules are proposed as probe radii instead of kinetic radius of N2 to well reflect pore volume in different sizes. The gas solubility does not simply follow the increasing trend of pore volume but is affected by the pore size and distribution, and large branch substitute groups is not the certain assurance of high gas solubility for material design.