Ion selective separators with the capability of conducting lithium ion and blocking polysulfides are critical and highly desired for high-performance lithium-sulfur (Li-S) batteries. Herein, we fabricate an ion selective film of covalent organic framework (denoted as TpPa-SO3Li) onto the commercial Celgard separator. The aligned nanochannels and continuous negatively charged sites in the TpPa-SO3Li layer can effectively facilitate the lithium ion conduction and meanwhile significantly suppress the diffusion of polysulfides via the electrostatic interaction. Consequently, the TpPa-SO3Li layer exhibits excellent ion selectivity with an extremely high lithium ion transference number of 0.88. When using this novel functional layer, the Li-S batteries with a high sulfur loading of 5.4 mg cm-2 can acquire a high initial capacity of 822.9 mA h g-1 and high retention rate of 78% after 100 cycles at 0.2 C. This work provides new insights into developing high-performance Li-S batteries via ion selective separator strategy.