Silicon oxide thin-film coated polymer substrates have great applications in the packaging industry for food and medical products, because these types of treated substrates show excellent barrier properties toward oxygen and moisture diffusion. In this work, silicon oxide coatings were fabricated on polyethylene terephthalate and polyimide (PI) substrates by an atmospheric pressure jet. The deposited coatings have been carefully characterized by Fourier Transform Infrared Spectroscopy, Scanning Electron Microscope and Atomic Force Microscope for chemical structures and morphology. The influence of the hexamethyldisiloxane concentration in feed gas and the distance from plasma nozzle to PI substrate is also carefully investigated. With optimized deposition conditions, the obtained silicon oxide coated PI substrates shows a satisfactorily low oxygen transmission rate of 0.7 ml/m2/day (at 25 °C, dry oxygen).