To meet the high requirements of future lithium secondary batteries based on lithium metal anodes for large-scale applications, we develop a cost-effective and environmentally friendly water-based method to prepare inorganic/polymer composite coating layers on commercial hydrophobic polyolefin-based microporous separators. To this end, we utilize a plasma-treatment technique. After the plasma treatment, the surface of the polyethylene (PE) separators changes from hydrophobic to hydrophilic, and the pore structures of the separators widen. These changes improve the affinity of the PE separators for polar liquid electrolytes and their ionic conductivities compared to those of bare PE and other ceramic-coated control systems. The polar functional groups derived from plasma treatment interact with the hydroxyl groups of water-soluble polymeric binders in the ceramic (Al2O3) coating layers, thereby improving the adhesion strength between the PE substrate and the ceramic coating layer. This improvement impedes hydrophobic recovery phenomena. As a result, plasma-treated ceramic-coated separators (plasma CCSs) exhibit superior power capability and cycle performance (plasma CCS maintained 94.7% of the initial discharge capacity up to the 1000th cycle at C/2, whereas bare PE’s remained high only up to the 300th cycle) in unit cells based on lithium metal anodes.