Featuring the art of covalent chemistry on 2D and 3D with molecular precision, covalent organic frameworks (COFs) have attracted immense interests from inorganic, organic, polymer, materials and energy chemistry. However, due to the synthetic challenge of âcrystallization problemâ, structural determination of COFs has been the bottleâneck in speeding up their discovery and design, as well as building up their structureâ property relation. Electron diffraction tomography (EDT) has been developed to determine crystal structures of COFs with only subâmicrometer sized single crystals, which enabled the ab initio determination of crystal structure, molecular connectivity, pore metrics, and hostâguest interaction at the atomic level. In this review, we summarized the recent developments of EDT for addressing challenges in structure determinations of such eâbeam sensitive, organic porous crystals, covering comprehensively automatic data collection, low dose, cryogenic protocols, structural solution method, powder Xâray diffraction refinement, and highâresolution transmission electron microscopy (HRTEM) imaging techniques. We do believe the EDT will propel this field into the new era of COF chemistry with atomic precision, and we envision the wide application of artificial intelligence will promote the structural determination and particle analysis of COFs and related materials.