In this study, Doppler broadening energy spectroscopy (DBES) combined with slow positron beam was used to discuss the effect of substrate types on the fine structure of a plasma-polymerized SiOCH layer as a function of depth. From the SEM pictures, the SiOCH films formed on different substrates showed hemispherical macrostructures, and the deposition rate was dependent on the mean pore size. It appears that the morphology of the plasma-polymerized SiOCH films was associated with the porosity-related characteristics of the substrate such as the size/shape of pores. As deposited on the MCE-022 substrate (mixed cellulose esters membrane with a mean pore size of 0.22 μm) with a nodular structure, the SiOCH films had pillar-like structures and high gas permeabilities. DBES results showed that the SiOCH films deposited on different substrates were composed of three layers: the SiOCH bulk layer, the transition layer, and the substrate. It was observed that the microstructure of the SiOCH films was affected layer by layer; a higher surface pore size in the substrates induced thicker transition layers with higher microporosities and led to thinner bulk layers having higher S parameter values during the plasma polymerization. It was also observed that the change in O2/N2 selectivity was consistent with the DBES analysis results. The gas separation performance and DBES analysis results agreed with each other.