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As a key component of lithium-ion batteries, a separator with excellent electrolyte wettability and good thermal stability has an important impact on the overall performance of lithium-ion batteries. Herein, a PVDF/sepiolite electrospun layer was coated on one side of the PP separator via electrospinning technology to prepare the composite separator (xMS-PVDF@PP) with sepiolite nanofibers modified with vinyltriethoxysilane (VTES) to ameliorate their dispersibility and compatibility with PVDF polymer matrix. The effect of modified sepiolite addition amounts on the physical and electrochemical properties of composite separator was intensively studied. It is found that the as-prepared xMS-PVDF@PP composite separator displays enhanced porosity, electrolyte uptake, thermal stability and Li+ ion transport kinetics than pristine PP separator. Specifically, Li|LiFePO4 battery with 20MS-PVDF@PP as separator shows the best rate and cycling performance, with a specific discharge capacity of 115.3 mAh·g–1 at 10C rate and a capacity retention rate of 97.06% after 200 cycles at 1C rate. The sepiolite in the electrospun layer can immobilize PF6– anion to facilitate the uniform distribution of Li+ ions and then inhibit the lithium dendrite growth, as well as absorb HF to alleviate Fe2+ dissolution from LiFePO4 cathode, thereby further improving the electrochemical performance of LiFePO4 battery.