Ion‐selective separators are promising to inhibit soluble intermediates shuttle in practical lithium‐sulfur (Li‐S) batteries. However, designing and fabricating such high‐performance ion‐selective separators using cost‐effective, eco‐friendly, and versatile methods remains a formidable challenge. Here we present ion‐selective separators fabricated via the spontaneous deposition of green tea‐derived polyphenols onto a polypropylene separator, aimed at enhancing the stability of Li‐S batteries. The resulting natural polyphenol‐reinforced ion‐selective (NPRIS24) separators exhibit rapid Li ion transport and high soluble intermediates inhibition capability with an ultralow shuttle rate of 0.67% for Li2S4, 0.19% for Li2S6 and 0.10% for Li2S8. This superior ion‐selectivity arises from the high electronegativity and strong lithiophilic nature of the phenolic compounds. Consequently, we have achieved high‐performance Li‐S batteries that are steadily cyclable under the challenging conditions of an S loading of 5.7 mg cm−2, an electrolyte‐to‐S ratio of 5.1 μL mg−1, and a 50 μm Li foil anode. Furthermore, the NPRIS24 separator enhances the performance of other Li metal batteries utilizing commercial LiFePO4 (5.3 mg cm−2) and LiNi0.5Co0.2Mn0.3O2 (9.9 mg cm−2) cathodes. This work underscores the potential of utilizing natural polyphenols for the design of advanced ion‐selective separators in energy storage systems.