Separators of current lithium ion batteries (LIBs) based on transition metal oxide cathodes need to be highly conductive for lithium ions but not for transition metal ions (TMIs). Herein, a novel polymer separator that can regulate the transportation of lithium ions and TMIs is reported, and it is fabricated by coating a custom-designed covalent organic framework (COF) from 1,3,5-tris(4-aminophenyl)benzene and 2,5-dimethoxybenzene-1,4-dialdehyde on a commercial polymer separator (PS). Electrochemical measurements combining physical characterization demonstrate that the lithium ion transference number (t_Li⁺) of the as-fabricated separator (PS@COF) is two times that of the uncoated PS, while the dissolved TMIs from cathodes are effectively isolated from anodes, leading to significantly enhanced cycling stability and rate capability of Li[Li_0.2Mn_0.55Ni_0.15Co_0.1]O₂ and LiNi_0.8Co_0.1Mn_0.1O₂-based LIBs. Theoretical calculations suggest that the COF provides the localized negatively charged groups (–OCH₃) for transporting lithium ions and the polar groups (–CN–) with lone pair electrons for chelating TMIs. Our strategy shares a perspective for performance improvement of LIBs and holds great promise for the application of covalent organic frameworks (COFs) in energy storage and conversion.