Conventionally, z-direction modulation of two-dimensional covalent organic frameworks (2D-COFs) is difficult to achieve because they rely on spontaneous pi-pi interactions to form 3D architectures. Herein, we report a facile construction of a novel intercalated covalent organic framework (Intercalated-COF) by synchronizing operations of supramolecular donor-acceptor (D-A) interactions (A unit: 2,5,8,11-tetra(p-formylphenyl)-perylene diimide (PDI) 1; D unit: perylene 3, as intercalator) in the vertical directions, with polymerizations (by only reacting 1 with p-phenylenediamine 2) in the lateral directions. In this Intercalated-COF, the PDI-based covalent 2D layers are uniformly separated by perylene guest layers. This supramolecular strategy opens the possibility for z-direction modulation of 2D-COFs through "intercalating" various guest molecules and thus may contribute to the exploration of advanced applications of these porous and crystalline frameworks.