ConspectusNanoporous crystals, such as silica mesoporous crystals (SMCs), zeolites, metal–organic frameworks (MOFs) and covalent organic frameworks (COFs), usually have unique geometrical features of periodically arranged pores from micro-, meso- to macro-scale. They have great potential to be structurally designed toward novel materials for various applications, such as storage, separation, and catalysis. In addition to the synthesis and applications of these materials, the structural analysis of nanoporous crystals is also critical for obtaining novel materials and unravelling their structure–property relationships. The crystal structure determines the pore size and connectivity of cages/channels, which are closely related to the performance of these materials in adsorption and catalysis. However, there are significant challenges in structural analysis due to small crystal size, electron-beam sensitivity, and local defects. Due to the strong interaction between electrons and matter, electron microscopy (EM) can provide rich structural information, which at the same time can also cause structural damage to samples. As early as 1960s, EM had been used to directly observe the lattice fringes of zeolites. Subsequently, the structures of many nanoporous crystals were solved and structural details such as defects, intergrowths, and surface structures were revealed by exploiting EM during the past decades. With the development of three-dimensional electron diffraction (3D ED) and low-dose high-resolution electron microscopy imaging, these approaches become more routine for solving the structure of nanocrystals and for revealing the local structural details. In this Account, we present our previous work on EM studies of several typical nanoporous materials, including SMCs, zeolites, MOFs, the TiO2@MIL-101 composite, and COFs. Various methods and strategies were developed and applied to different materials based on the characteristics of their structures. For example, 3D electrostatic potential maps of SMCs can be reconstructed by Fourier synthesis of crystal structure factors obtained from high-resolution TEM images, leading to the discovery of many 3D mesostructures. New zeolites/MOFs/COFs structures, which were not previously solved due to their structural complexity and small crystal size, have been determined using 3D ED data from nanosized crystals or using a combination of electron diffraction and high-resolution imaging. In addition, EM methods for determining the handedness of nanocrystals have also been developed and successfully applied to SMCs and STW zeolite based on high-resolution EM imaging or dynamical electron diffraction. Recently, a new strategy involving a combination of 3D ED and cryogenic protocol was proposed to study the structure, dynamics, and the host–guest interactions in a COF material. The direct-space strategy for structure solution, implemented using a genetic algorithm, was also demonstrated to be a successful approach for solving structures from low-resolution 3D ED data. By now, EM has become one of the most widely used methods in the study of nanoporous materials. We hope this Account will promote further developments of EM and stimulate the design and synthesis of new functional nanoporous materials.