Lithium–sulfur batteries (LSBs) have attracted widespread attention due to their high theoretical energy density. However, the dissolution of long-chain polysulfides into the electrolyte (the “shuttle effect”) leads to rapid capacity decay. Therefore, finding suitable materials to mitigate the shuttle effect of polysulfides is crucial for enhancing the electrochemical performance of lithium–sulfur batteries. In this study, LSBs’ separator is modified with Ni3V2O8 nanoparticles@carboxylated carbon nanotubes (Ni3V2O8@CNTs) composite. There are abundant oxygen vacancies in Ni3V2O8@CNTs composite which plays a synergistic effect on shuttle effect. The Ni3V2O8 can tightly anchor soluble polysulfides through oxygen vacancies, while the CNTs not only facilitate the transport of ions and electrons but also weaken the migration of polysulfides, limiting shuttle effect. As a result, the cycling stability of LSBs using Ni3V2O8@CNTs-modified separator has been significantly improved (with a capacity decay rate of only 0.0334% after 1500 cycles at 4.0C). This study proposes a strategy to design modified separator for high-performance LSBs.