Metal‐organic frameworks (MOFs) and covalent organic frameworks (COFs) are two emerging families of functional materials that have found widespread applications in various fields. With the unique features of large surface area, tunable pore structure, high porosity, and easy surface functionalization, they are considered a kind of promising separators candidates for novel separators in rechargeable batteries. Over the years, many studies on the application of MOF/COF‐based separators have been reported with excellent performance. Herein, we highlight the recent progress of MOF/COF separators for advanced batteries. Firstly, the key properties of MOF/COF separators are presented. Then, we summarize the fabrication methods of MOF/COF separators. Afterward, an overview of the applications of MOF/COF based separators in lithium‐based batteries, sodium‐based batteries, and other secondary batteries. Finally, we present a summary and future outlook of MOF/COF separators, including their potential and current challenges.