Abstract Covalent organic frameworks (COFs) have received great attention as electrode materials in the lithium‐ion batteries due to their exceptional crystallinity, easily chemical modification, and adjustable porous distribution. However, their practical application remains hindered by the insufficient Li + active sites and long ion diffusion in the bulk materials. To tackle those issues, combining the virtues of high stable skeleton structure of large molecular, atomic‐layer thickness feature, and multi‐active sites, a novel atomic‐layer COF cathode (denoted as E‐TP‐COF) with a dual‐active‐center of CO and CN group is developed. The atomic‐layer thick structure improves the capturing and diffusion of Li‐ion. Both active sites of CN and CO groups generate more capacity. The large molecular structure avoids the dissolubility challenge in electrolytes. As a result, the lithium‐ion batteries assembled with E‐TP‐COF delivers a high initial capacity of 110 mAh g −1 with a high capacity retention of 87.3% after 500 cycles. Furthermore, the Li + diffusion mechanism is also confirmed through in(ex) situ technology and density functional theory calculation in detailing. This new strategy may exploit an important application of COFs in electrochemical energy storage and conversion.