Heterogeneous catalysts are the most important catalysts in industrial reactions. Nanocatalysts, with size ranging from hundreds of nanometers to the atomic scale, possess activities that are closely connected to their structural characteristics such as particle size, surface morphology, and three-dimensional topography. Recently, the development of advanced analytical transmission electron microscopy(TEM) techniques, especially quantitative high-angle annular darkfield(HAADF) imaging and high-energy resolution spectroscopy analysis in scanning transmission electron microscopy(STEM) at the atomic scale, strengthens the power of(S)TEM in analyzing the structural/chemical information of heterogeneous catalysts. Three-dimensional reconstruction from two-dimensional projected images and the real-time recording of structural evolution during catalytic reactions using in-situ(S)TEM methods further broaden the scope of(S)TEM observation. The atomic-scale structural information obtained from high-resolution(S)TEM has proven to be of significance for better understanding and designing of new catalysts with enhanced performance.