Covalent organic frameworks (COFs) are promising porous materials due to their high specific surface area, adjustable structure, highly ordered nanochannels, and abundant functional groups, which brings about wide applications in the field of gas adsorption, hydrogen storage, optics, and so forth. In recent years, COFs have attracted considerable attention in electrochemical energy storage and conversion. Specifically, COF‐based functional separators are ideal candidates for addressing the ionic transport‐related issues in high‐energy batteries, such as dendritic formation and shuttle effect. Therefore, it is necessary to make a comprehensive understanding of the mechanism of COFs in functional separators. In this review, the advantages, applications as well as synthesis of COFs are firstly presented. Then, the mechanism of COFs in functional separators for high‐energy batteries is summarized in detail, including pore channels regulating ionic transport, functional groups regulating ionic transport, adsorption effect, and catalytic effect. Finally, the application prospect of COFs‐based separators in high‐energy batteries is proposed. This review may provide new insights into the design of functional separators for advanced electrochemical energy storage and conversion systems.