Electron microscopy and its associated techniques have contributed significantly to the characterization of heterogeneous catalysts, especially supported metal catalysts, and can provide nano- or atomic-scale information on the structure, morphology, composition, and electronic state of the area of interest. With the recent advancement in aberration corrections to achieve an image resolution below 0.1 nm and the rapid development of in situ techniques, advanced electron microscopy is poised to probe fundamental questions of heterogeneous catalysis and catalysts. Understanding the nature of metal–support interactions becomes critical if we want to achieve the goal of designing and fabricating nanoarchitectured catalysts with desired performances. To reliably probe the fundamental mechanisms of charge transfer, which is the core of catalysis, between individual nanoscale components and under a realistic gas environment and temperature is still a formidable challenge. This Review discusses the recent contribution of advanced electron microscopy to the study of metal–support interactions, as well as the challenges and opportunities of applying aberration-corrected electron microscopy techniques to the investigation of atomic-scale structures of complex heterogeneous catalysts.