Lithium–sulfur (Li–S) batteries have been considered as a prospective candidate of secondary high-energy storage systems, but the shuttle effect of polysulfides through separator is a vital challenge for battery development. Herein, we report a facile strategy to modify commercial polypropylene (PP) separator by depositing a laminar MXene-Nafion composite. Nafion, as a surfactant, results in an ordered layer-by-layer deposition of MXene sheets by filtration. By comparing this modification layer to references composed of Nafion and MXene, we demonstrate that the physical resistance of MXene and electrostatic repulsion of Nafion can synergistically inhibit the shuttle effect. And the resultant Li–S cell shows exceptional cycling stability: ultralow capacity decay of 0.03% per cycle over 1000 cycles at 1C. Furthermore, MXene promotes the re-utilization of polysulfides due to its electrical conduction, while Nafion in interlayer effectively transports Li+. Thus, the cell achieves highly enhanced initial capacity (1234 vs. 834 mAh g−1 for PP cell). Besides, these results are also much higher than that of a dual-layer modification layer (MXene@Nafion), highlighting the full synergism of organic and inorganic components in this laminar nanostructure. Moreover, the laminar GO-Nafion as an example verifies the universality of this design strategy.