Monte Carlo simulation of deposition of nonstoichiometric amorphous SiOx nanolayers from vapor phase onto a polymer surface is reported. The model developed is based on the network properties of silica and takes into account dangling bonds arising during the real process of deposition. The model is validated via comparison of the radial- and bond angle distribution functions for the simulated Si and SiO2 structures with those obtained from experiment for bulk materials. Porosity of the simulated amorphous layer is characterized by the relative volume of pores and the ratio of the pore surfaces to the pore volume. We found that porosity strongly depends on nucleation sites density (NSD) on the polymer substrate. At NSD lower than 1 nm−2 the porosity may reach as much as 30% of the layer volume, while at NSD higher than 4 nm−2 it decreases down to 3-7%. Possible implications of the obtained results are discussed.