Zeolites are a class of inorganic microporous crystalline materials with ordered pore channels, unique shape selectivity, adjustable acidity and alkalinity, and high stability and have been widely used in gas adsorption and heterogeneous catalysis. The size of the zeolite pore structure determines its molecular sieving properties. Therefore, flexibly adjusting the zeolite pore structure and the host-guest interactions with guest molecules to control diffusion or reaction pathways is crucial for designing novel zeolites. Observing the real movement behavior of small molecules and changes in the local structure of the zeolite framework at the micro-nano scale is of great significance. Recently, emerging scanning transmission electron microscopy (STEM) imaging techniques, such as integrated differential phase contrast/optimum bright-field STEM (iDPC/OBF-STEM) and 4D-STEM ptychography have shown great potential for atomic resolution characterization of zeolites, since these are greatly advantageous for imaging electron beam-sensitive materials and light elements. This review first introduces the structural characteristics and applications of zeolites. Secondly, we discuss the application of three emerging imaging techniques in atomic imaging of zeolites. Thirdly, we focus on using iDPC-STEM imaging technology to observe the host-guest interactions between zeolites and single molecules (e.g., benzene, p-xylene, and pyridine). Furthermore, we explore the adsorption-desorption behavior of single molecules in zeolites using in situ iDPC-STEM imaging technology. Finally, we discuss the current challenges and future prospects of advanced TEM characterization techniques in the imaging of zeolite-confined single molecule.