We demonstrate a facile approach for the fabrication of new silica (SiO2) nanoparticles/polyvinylidene fluoride-hexafluoropropylene (PVdF-HFP)-coated polyethylene terephthalate (PET) nonwoven composite separators for use in lithium-ion batteries. By varying the SiO2/PVdF-HFP composition ratio, we can fine-tune the porous structure of the composite separators. At a low SiO2/PVdF-HFP ratio, a nonporous structure featuring the PVdF-HFP matrix and SiO2 domains is obtained. By contrast, an unusual porous structure (i.e., highly-percolated interstitial voids formed between close-packed SiO2 nanoparticles) is developed at a high SiO2/PVdF-HFP ratio, where PVdF-HFP serves as a binder to interconnect SiO2 powders. This drastic change in the morphology of the composite separators is further confirmed by observing their air permeability and ionic conductivity. Meanwhile, a PET nonwoven is employed as a mechanical substrate to suppress thermal shrinkage of the composite separators. On the basis of morphological characterization, the effects of the composition ratio-dependent structural evolution of the composite separators on the electrochemical performance of cells are investigated. Notably, the composite separator fabricated from a composition ratio of SiO2/PVdF-HFP=90/10 (wt%/wt%) provides superior cell performance owing to a well-tailored microporous structure, as compared to a commercialized polyethylene (PE) separator.