The oxygen transmission rate (OTR) of SiOx coated polyethylene terephthalate (PET) and biaxially oriented polypropylene (BOPP) affected by fine defects is discussed in this paper. With an ultrasonic AFM (UAFM), which is an advantageous to distinguishing tiny defects on/ in the deposited films, it is found that the OTR of the coated films is relevant to the morphology scanned by UAFM. Herein SiOx layers with a thickness in the order of nano-scale were fabricated in 13.56 MHz-radio frequency (RF) -plasma-enhanced chemical vapor deposition (PECVD). The monomer for the coating fabrication is hexamethyldisiloxane (HMDSO). Fourier transform inferred (FTIR) spectra of the deposited coating with a strong peak at 1062 cm-1, corresponding to Si-O-Si stretching vibration, confirm the formation of SiOx coatings through PECVD. The higher OTR value of SiOx coated PET is consistence with defects on film surface and in the subsurface of coatings through UAFM. It obtains that the OTR value of the defect free SiOx coated film was reduced by ca. 89% compared with the defect existence SiOx coated PET.