Radicals are inevitable intermediates during the charging and discharging of organic redox electrodes. The increase of the reactivity of the radical intermediates is desirable to maximize the capacity and enhance the rate capability but is detrimental to cycling stability. Therefore, it is a great challenge to controllably balance the redox reactivity and stability of radical intermediates to optimize the electrochemical properties with a good combination of high specific capacity, excellent rate capability, and long-term cycle life. Herein, we reported the redox and tunable stability of radical intermediates in covalent organic frameworks (COFs) considered as high capacity and stable anode for sodium-ion batteries. The comprehensive characterizations combined with theoretical simulation confirmed that the redox of C-O center dot and alpha-C radical intermediates play an important role in the sodiation/desodiation process. Specifically, the stacking behavior could be feasibly tuned by the thickness of 2D COFs, essentially determining the redox reactivity and stability of the alpha-C radical intermediates and their contributive capacity. The modulation of reversible redox chemistry and stabilization mechanism of radical intermediates in COFs offers a novel entry to design novel high performance organic electrode materials for energy storage and conversion.