Covalent organic frameworks (COFs) have wide‐ranging applications, and their host–guest interactions play an essential role in the achievement of COF functions. To investigate these host–guest interactions, it is necessary to locate all atoms, especially hydrogen atoms. However, it is difficult to determine the hydrogen atomic positions in COFs because of the complexities in synthesizing high‐quality large single crystals. Three‐dimensional electron diffraction (3D ED) has unique advantages for the structural determination of nanocrystals and identification of light atoms. In this study, it was demonstrated for the first time that the hydrogen atoms of a COF, not only on the framework but also on the guest molecule, can be located by 3D ED using continuous precession electron diffraction tomography (cPEDT) under cryogenic conditions. The host–guest interactions were clarified with the location of the hydrogen atoms. These findings provide novel insights into the investigation of COFs. The hydrogen atoms of a covalent organic framework on the framework and guest molecules were located using cryo‐3D electron diffraction for the first time. The host–guest interactions in the framework material were clarified by locating the hydrogen atoms.