Metal–organic frameworks (MOFs) are crystalline porous materials with designable topology, porosity and functionality, having promising applications in gas storage and separation, ion conduction and catalysis1,2,3. It is challenging to observe MOFs with transmission electron microscopy (TEM) due to the extreme instability of MOFs upon electron beam irradiation4,5,6,7. Here, we use a direct-detection electron-counting camera to acquire TEM images of the MOF ZIF-8 with an ultralow dose of 4.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM reveals important local structural features of ZIF-8 crystals that cannot be identified by diffraction techniques, including armchair-type surface terminations and coherent interfaces between assembled crystals. These observations allow us to understand how ZIF-8 crystals self-assemble and the subsequent influence of interfacial cavities on mass transport of guest molecules.