The energy density and power of lithium-ion batteries (LIBs) are undoubtedly essential to fuel the satisfying pursuit of next-generation energy storage systems. However, to ensure the safety of LIBs, a micrometer-thick ceramic coating layer (CCL) is coated on the separator by a conventional slurry process, which reduces the energy density and performance of LIBs. For this purpose, a ceramic-coated separator (CCS) fabricated by sputtering has attracted attention because it can secure thermal stability and performance while minimizing the CCL thickness to nanometers. Nevertheless, the analysis of why a CCL with only nanometer thickness could improve the properties of the separator still needs to be investigated. Theoretically, it could be suggested that sputtered nano ceramic particles could penetrate the internal micropore structure of the separator, but no experiments were conducted to identify this. In this study, depth profiling using time-of-flight secondary ion mass spectrometry was conducted to confirm the distribution of sputtered nano ceramic particles in the internal structure of the separator depending on the porosity. The surface composition of the separator changed by the plasma generated during the sputtering process was observed by X-ray photoelectron spectroscopy. In addition, to investigate the effect of the nm-CCL on the properties and electrochemical performance of the separator, we compared it with commercial slurry CCS and single/double-sided ceramic sputtering samples.