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The implementation of a functional separator represents a highly encouraging approach to mitigating polysulfide shuttling in lithium–sulfur (Li–S). In this study, a two-dimensional (2D) 1,3,5-triformylphloroglucinol (Tp)-p-phenylenediamine (Pa) covalent organic framework/reduced graphene oxide (rGO) functional layer was introduced to enhance the performance of the commercial separator in Li–S batteries. The resulting 2D TpPa@rGO modified separators exhibit significantly improved electronic and ionic conductivity when compared to the unmodified separator, effectively mitigating lithium polysulfide shuttling and enhancing sulfur cathode utilization. It is indicated that a heterostructured composite of a nitrogen-group-containing COF and an electronic conductive addictive is an effective modification to the separator. Consequently, the modified cell demonstrated a minimal degradation rate of only 0.12% per cycle over 350 cycles at 0.5 C.