In the present work, Fe-montmorillonite was synthesized by hydrothermal method, and then was modified by cetyltrimethyl ammonium bromide (CTAB). The polyamide6 (PA6) nanofibers and PA6/organic-modified Fe-montmorillonite (Fe-OMT) nanocomposite fibers were firstly prepared by a facile compounding process with electrospinning, and then coated by silicon nanoparticles (Si) using magnetron sputter technique. The High-resolution transmission electron microscopy (HRTEM) image indicated that the silicate clay layers were well dispersed within the nanocomposite fibers and aligned almost along the axis of the nanofibers. The influences of the Si sputter coating on structures, surface morphology, thermal and flammability properties of PA6 nanocomposite fibers were characterized by Scanning electron microscope (SEM), Energy dispersive X-ray spectroscopy (EDX), X-ray photoelectron spectroscopy (XPS), Atomic force microscope (AFM), Thermogravimetric analyses (TGA) and Micro Combustion Calorimeter (MCC), respectively. The SEM images showed that the diameters of nanocomposite fibers were decreased with the loadings of the Fe-OMT, and the Si thin film with nanoparticles were well coated on the surface of homogeneous and cylindrical nanofibers. The EDX analyses confirmed the presences of the Fe-OMT and Si nanoparticles on the nanofibers. The XPS spectra reflected the chemical features of the deposited nanostructures. The AFM observations revealed a remarkable difference in the surface morphology of nanocomposite fibers after sputter coating. The TGA analyses indicated the barrier effects of silicate clay layers, catalysis effect of Fe³⁺ and synergistic effects between the Fe-OMT and Si improved thermal stability properties of the coated nanocomposite fibers. It was found from the MCC tests that the peak of heat release rate (PHRR) of the coated nanocomposite fibers decreased significantly, contributing to the improved flame retardant properties.