AbstractRoom‐temperature sodium–sulfur (RT/Na–S) batteries are a promising low‐cost energy storage technology. However, the vital role of the separator in the system is often overlooked. Inspired by the maintenance of brain homeostasis by human brain capillaries, this work pioneers a host–guest self‐assembled strategy for covalent organic scaffold membranes, endowing the membrane with multiple functions (sodium ion transport, confinement, and conversion of polysulfides) to maintain the stability of the RT/Na–S battery system. The free‐standing multifunctional covalent organic framework membrane (HB/CNT@COF) maximizes the roles of the host framework and guest molecules. Because of the synergistic effect of hydroxynaphthol blue (HB) and multiwalled carbon nanotubes (CNT), the HB/CNT@COF cell exhibits a capacity of 733.4 mAh g−1 with limited capacity fading after 400 cycles at 4 C. This performance is nearly four times that of commercial glass fiber separators. Additionally, the cell demonstrates excellent performance under electrolyte‐poor conditions.