Heterogeneous catalysis is one of the oldest nanosciences. Although model catalysts can be designed, synthesized, and, to a certain degree, characterized, industrial heterogeneous catalysts are often chemically and physically complex systems that have been developed through many years of catalytic art, technology, and science. The preparation of commercial catalysts is generally not well controlled and is often based on accumulated experiences. Catalyst characterization is thus critical to developing new catalysts with better activity, selectivity, and/or stability. Advanced electron microscopy, among many characterization techniques, can provide useful information for the fundamental understanding of heterogeneous catalysis and for guiding the development of industrial catalysts. In this article, we discuss the recent developments in applying advanced electron microscopy techniques to characterizing model and industrial heterogeneous catalysts. The importance of understanding the catalyst nanostructure and the challenges and opportunities of advanced electron microscopy in developing nanostructured catalysts are also discussed.