Layer-stacking behaviors are crucial for two-dimensional covalent organic frameworks (2D COFs) to define their pore structure, physicochemical properties, and functional output. So far, fine control over the stacking mode without complex procedures remains a grand challenge. Herein, we proposed a “key-cylinder lock mimic” strategy to synthesize 2D COFs with a tunable layer-stacking mode by taking advantage of ionic liquids (ILs). The staggered (AB) stacking (unlocked) COFs were exclusively obtained by incorporating ILs of symmetric polarity and matching molecular size; otherwise, commonly reported eclipsed (AA) stacking (locked) COFs were observed instead. Mechanistic study revealed that AB stacking was induced by a confined interlocking effect (CIE) brought by anions and bulky cations of the ILs inside pores (“key” and “cylinder”, respectively). Excitingly, this strategy can speed up production rate of crystalline powders (e.g., COF-TAPT-Tf@BmimTf2N in merely 30 minutes) under mild reaction conditions. This work highlights the enabling role of ILs to tailor the layer stacking of 2D COFs and promotes further exploration of their stacking mode-dependant applications.