In this work, low frequency PECVD a-SiCxNy:H thin films have been synthesized in the temperature range 25–300 °C from hexamethyldisilazane precursor mixed with ammonia at various concentrations. A relevant correlation has been evidenced between the [N]/[C] atomic ratio in the gaseous phase and in the deposited thin films, allowing both prediction and control of the film microstructure. A simple method based on the analysis of the films FTIR spectra was proposed to determine the value of the [N]/[C] ratio and thus predict or adjust the gas transport properties of the membrane materials. Attractive ideal selectivities α*He/N2 exceeding 90 with He permeance ΠHe > 3.10−7 mol.s−1.m−2.Pa−1 were measured at 150 °C for the films prepared at 300 °C with an optimum [N]/[C] atomic ratio in the range 0.1–1.5. These films behave as molecular sieve membranes with a thermally activated transport of helium.