Abstract Aqueous zinc–iodine batteries show immense potential in the electrochemical energy storage field due to their intrinsic safety and cost‐effectiveness. However, the rampant dendritic growth and continuous side reactions on the zinc anode, coupled with the shuttling phenomenon of polyiodides, severely affect their cyclic life. In response, this study utilizes a carboxyl‐functionalized metal‐organic framework UiO‐66‐(COOH) 2 (UC) to modify commercial glass fiber (GF) to develop a novel ionic selective separator (UC/GF). This separator exhibits cation exchange ability for Zn 2+ and polyiodides, thereby simultaneously stabilizing the zinc anode and inhibiting the shuttle effect of polyiodides. Enhanced by the abundant polar carboxyl groups, the UC/GF separator can effectively facilitate Zn 2+ ion transport and accelerate the desolvation of hydrated zinc ions by its zincophilicity and hydrophilicity, while significantly hindering the transfer of polyiodides via electrostatic repulsion. Consequently, the Zn|UC/GF|Zn symmetric battery enables a long lifespan of over 3400 h at a current density of 5.0 mA cm −2 , while the Zn|UC/GF|I 2 exhibits an exceptional discharge capacity of 103.8 mAh g −1 after 35 000 cycles at 10 C with a capacity decay rate of only 0.0013% per cycle. This separator modification strategy that synergistically optimizes anode and cathode performance provides unique insights into the commercialization of zinc–iodine batteries.