An SiOxCyHz/mixed cellulose ester (MCE) composite membrane was fabricated by plasma deposition of hexamethyldisiloxane (HMDSO) monomer on the surface of an MCE substrate. The purpose is to apply the membrane for the oxygen enrichment of an O-2/N-2 mixture. The variation in the fine structure of the plasma-polymerized layers (SiOxCyHz) prepared at different plasma conditions was identified using slow-positron beams. Although the SiOxCyHz layers displayed similar FTIR spectra, they evidently showed differences based on the data from Doppler broadening energy spectroscopy (DBES) and positron annihilation lifetime spectroscopy (PALS). These data indicated distinct differences in the physical structure despite the similarities in the chemical structure of the films. The deposited layer (mixture of HMDSO species and MCE species) had more hydrocarbon group, resulting in a looser structure of the deposited layer at the initial period of plasma deposition. However, the MCE species content of the deposited layer decreased with the deposition time, and the deposited layer became denser. From PALS, the o-Ps lifetime (tau(3), corresponding to the free-volume size) decreased along the plasma deposition layer growth direction. These results corresponded with those obtained from XPS very well. The plasma-deposited membrane was applied for O-2/N-2 separation. The O-2 permeability decreased and the concentration of O-2 in the permeate increased with the deposition time and as the plasma power increased.