Non-woven mats of thermally stable polyimide (PI) composites were fabricated as a separator of lithium-ion batteries (LIBs) by first electrospinning a mixture of the pre-polymer, poly(amic acid) ammonium salt (PAAS), and inorganic nanoparticles of SiO2 or Al2O3 and then imidizing the electrospun nanofibers of the PAAS composites at 350°C. The microstructures of the electrospun PI nanofibers, electrospun PI–SiO2-composite nanofibers, electrospun PI–Al2O3-composite nanofibers, and the commercial separator SV718 were examined using field-emission scanning electron microscopy and transmission electron microscopy. Test results of the thermal properties of the PI nanofibers, PI-composite nanofibers, and SV718, obtained with a thermal gravimetric analyzer and a differential scanning calorimeter, indicate the superior thermal stability of PI and PI composites, which showed no melting peak and no decomposition at 600°C, while SV718 had a melting peak at 137°C and decomposed at 300°C. The thermal stability of the separators, evaluated in a hot-oven test, showed no shrinkage of PI and PI composites at 200°C, while SV718 started to shrink at above 100°C. Using a drop of liquid electrolyte on the surface of each separator, the electrolyte contact angle on PI and PI composites was around 10° and that on SV718 was 54°, indicating that PI and PI composites had better wettability than SV718. The porosity and liquid-electrolyte uptake of the PI composites were over 90% and 790%, respectively, while the corresponding values for SV718 were 40% and 101%, respectively, implying that the separators consisting of the non-woven mats of PI–SiO2-composite nanofibers and PI–Al2O3-composite nanofibers had lower interfacial resistance than the commercial SV718 separator. The electrochemical performance of the PI-composite separator assembled between the LiCoO2 cathode and the Li anode of an LIB exhibited more stable cycle performance, higher discharge capacity, and better capacity retention compared with those using the SV718 separator. Hot oven test for the charge cells at 150°C, the PI and PI-composite separator showed better thermal stability than SV718.