Understanding the dynamics of covalent organic frameworks (COFs) is desirable for developing smart materials with coherent responses to external stimulus. Here we illustrate the structural determination of dynamics at atomic level by cryo-electron diffraction tomography (EDT) with single crystals of COF-300 having only submicrometer sizes. We observe and elucidate the crystal contraction upon H2O adsorption by ab initio structural solution of all non-hydrogen atoms of framework and unambiguous location of guest molecules in the pores. We also observe the crystal expansion of COF-300 upon inclusion of ionic liquid or polymer synthesized in the channels, whose conformational aspects of frameworks can be confirmed.