The development of high-performance separators is urgently needed to improve the safety and electrochemical performance of high-energy-density lithium metal batteries (LMB). Poly (ether ether ketone) (PEEK) is an ideal separator candidate due to its high chemical resistance and excellent thermal stability. However, the processing of PEEK for separators with proper porous structure is rather challenging. Beyond the conventional sulfonation process of PEEK, here, a reversible chemical modification strategy is exploited to fabricate heat-resistant PEEK separators with sophisticated hierarchical pore architecture. The lyophilic PEEK separators including dense surface layers, middle layers with horizontally aligned pore arrays, and honeycomb-structured bottom layers enable fast ion transport and uniform Li