In industry, membrane separation of gas mixtures is of considerable significance. For example, the composite poly (4-methyl-2-pentyne) (PMP) and silica nanoparticle is used to separate C4H10 (n-butane) from mixtures of C4H10 and CH4, H-2, etc. Silica has different crystalline forms. The transport properties of penetrants in the composite PMP and nanoparticles of cristobalite silica (PMPC) and the composite PMP and nanoparticles of faujasite silica (PMPF) are different. It is essential to explore this difference from the molecular level in order to have an in-depth knowledge and aid the design of the membrane based on composite PMP and silica nanoparticles. In this work, the molecular dynamics (MD) method was employed to explore the transport of different penetrants in the composites of PMP and nanoparticles of two forms of silica. The simulation results show that both types of composites have high permeability compared with PMP for the same penetrants and PMPF has higher permeability than PMPC for the same penetrants. The selectivity of n-C4H10 over CH4 in PMPF, on the contrary, is lower than in PMPC. Finally, the influence of weight concentration of nanoparticle in PMPC on selectivity of n-C4H10 over CH4 was explored.