Over the past two decades, covalent organic frameworks (COFs) have become the most widely studied porous crystalline materials. Their specific physical and chemical properties are determined by the arrangement of atoms (crystal structure). Therefore, the determination of their structure is arguably the most important characterization step for COFs. Although single-crystal X-ray diffraction is the most widely used method for structure determination, confirmation of the structure of COFs is limited to lattice fringes in transmission electron microscopy (TEM) because of their small crystal size (nanocrystals) or poor crystal quality. At present, many two-dimensional COFs (2D-COFs) have clear powder X-ray diffraction (PXRD) patterns, but specific lattice fringes are not available for all 2D-COFs. This severely hinders the development of the COF field. Here, we discovered the lattice shrinkage behavior of COFs under electron beam irradiation by comparing the lattice fringes of 2D-COFs under different conditions. By comparing the lattice fringes of a 1,3,5-tris-(4-aminophenyl)triazine-1,3,5-tris-(4-formylphenyl)triazine covalent organic framework (TAPT-TFPT COF) at room temperature and under liquid nitrogen freezing conditions, we found that the lattice fringes are in good agreement with the PXRD and the theoretical values of the COF (2.213 nm) under freezing conditions. However, the lattice fringe spacing is only 1.656 nm at room temperature. The discovery not only provides new insights into the TEM characterization of COFs, but also further expands the range of crystalline COF materials.