The hydroxyl groups in inorganic-organic hybrid poly (cyclotriphosphazene-co-4,4-sulfonyldiphenol) (PZS) exhibits some reactivity toward lithium ions. In this work, the core-shell structured silica-poly (cyclotriphosphazene-co-4,4′-sulfonyldiphenol) nanoparticles (SiO2-PZS) are synthesized and the composite separator is prepared by coating on both sides of polyethylene (PE) microporous membrane. Compared to pure SiO2 coated separator and PE membrane, the PE-SiO2@PZS separator shows higher ionic conductivity. The corresponding discharge capacity at 8C rate reaches a value of 115 mA h g−1, compared to 105 mA h g−1 for PE membrane and 106 mA h g−1 for PE-SiO2 separator. The hydroxyl group and N、O atoms on the surface of PZS can coordinate with lithium ions to enhance the dissociation of lithium salt (LiPF6), thus improving the ionic conductivity and discharge capacity. Meanwhile the lower interfacial impedance resistance for PE-SiO2@PZS separator indicates intimate adhesion between electrode and separator. In a word, the SiO2-PZS nanoparticles are a promising filler for enhancing the wettability and electrochemical performance of Lithium-ion battery separator.