Li dendrite and the shuttle effect are the two primary hindrances to the commercial application of lithium-sulfur batteries (LSBs). Here, a multifunctional separator has been fabricated via successively coating carbon nanotubes (CNTs) and lithium phytate (LP) onto a commercial polypropylene (PP) separator to improve the performance of LSBs. The LP coating layer with abundant electronegative phosphate group as permselective ion sieve not only reduces the polysulfide shuttle but also facilitates uniform Li+ flux through the PP separator. And the highly conductive CNTs on the second layer act as a second collector to accelerate the reversible conversion of sulfide species. The synergistic effect of LP and CNTs further increases the electrolyte wettability and reaction kinetics of cells with a modified separator and suppresses the shuttle effect and growth of Li dendrite. Consequently, the LSBs present much enhanced rate performance and cyclic performance. It is expected that this study may generate an executable tactic for interface engineering of separator to accelerate the industrial application process of LSBs.