Zeolites have received great attention due to their wide applications in various fields such as catalysis, adsorption/separation, ion exchange, etc. Determining the atomic crystal structure of zeolites is crucial to understanding their functions and exploring their applications. Due to the difficulty of synthesizing large single crystals, the structures of many zeolites cannot be solved using conventional single-crystal X-ray diffraction (SCXRD) methods. Three-dimensional electron diffraction (3D ED) has witnessed rapid development during the past decade and has shown its powerful ability in the structure determination of zeolites. In this review, we will briefly introduce the history of 3D ED and summarize recent advances in the application of 3D ED for the analysis of zeolite structures, along with several typical examples in this research field.