Two types of non-aqueous ceramic-coated separators, based on Al2O3 and Mg(OH)2, with extremely high thermal stability are prepared at a pilot scale. To investigate the factors determining the electrochemical and safety performance of the battery, the structure and properties of Al2O3 and Mg(OH)2 separators are characterized at the entire separator and coating-layer level using nanoindentation. Both separators exhibit almost 0% thermal shrinkage, even at 200 °C, and good electrolyte wettability. The mechanical properties of the coating layers, represented as indentation modulus and hardness, reveal that the Mg(OH)2 separator is more flexible than Al2O3 separator, which is brittle, and exhibits a trend of hardness strengthening with increasing penetration depth. These mechanical properties of the coating layer of separators dominantly affect nail penetration more than electrochemical performance. Electrochemical performance is affected more by the uniformity and electrochemical stability of the ceramic/binder coating layer. Indeed, Al2O3 and Mg(OH)2 cells show similar value of capacity retention of 78.6 and 77.8% after 1100 cycles, and internal resistance of 128.5 and 132.0%, respectively. Pouch cells equipped with Mg(OH)2 separators do not show any events, evaluated as L3, while Al2O3 separator-incorporated cells are evaluated as L6 during the nail penetration test.