Knowing the structure of porous materials is essential for understanding their properties and exploiting them for applications. Electron crystallography has two main advantages compared to X-ray diffraction for structure determination. Crystals too small or too complicated to be studied by X-ray diffraction can be studied by electron crystallography. The crystallographic structure factor phase information, which is lost in X-ray diffraction, can be obtained from high-resolution transmission electron microscopy (HRTEM) images. Here, different electron microscopic techniques and their applications for structure determination of porous materials are reviewed. The recently developed automated diffraction tomography (ADT), the rotation electron diffraction (RED), and the through-focus structure projection reconstruction (QFcous) methods make the structure determination by electron crystallography more feasible for non-TEM experts and as efficient as that by X-ray diffraction. How the various electron crystallographic methods are chosen are demonstrated and these methods used for solving different structural problems in porous materials. The benefits of combining electron crystallography and X-ray diffraction for studying complex zeolite structures are also shown. A large number of examples are given to demonstrate the use of various electron crystallographic techniques for structure determination of zeolites, metal-organic frameworks and ordered mesoporous materials. These electron crystallographic methods are general and can also be used for structural studies of other functional materials.