In this study, poly(ethylene terephthalate) (PET) nonwoven fabrics were used as substrates for creating functional nanostructures on the fiber surfaces. Magnetron sputtering was employed to deposit transparent and conductive indium-tin-oxide (ITO) nanofilms onto the nonwoven fabrics. The effects of the various deposition conditions on the surface and interfacial nanostructures were investigated by scanning electron microscopy (SEM), atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). AFM observations revealed the effect of the deposition conditions on the morphology of the fibers. Surface chemical structures of the functional nonwoven fabrics were confirmed by XPS analysis. The interfacial structures were revealed by SEM examinations. The adhesion of the ITO coating to the fabric was investigated by the peel-off test. It was found that plasma pretreatment and heating during the sputter coating process obviously improved the adhesion of ITO coating to the PET fibers.