Zeolites are a family of nanoporous crystalline materials with ordered channel systems, flexibly adjustable activity, and high hydrothermal stability and have been widely used as adsorbents and catalysts. The micropores of zeolites are comparable to the size of single molecules, which can function as "molecular sieves" by selectively adsorbing or transforming targeted guest molecules. Therefore, a slight mismatch in the dimensions of the pore architecture and guest molecules sometimes will cause thousands of times of changes in the physicochemical processes inside zeolite channels. Adjusting the pore structures to match targeted molecules to precisely regulate the host−guest interactions between them and thereby control the diffusion or reaction pathways has always been one of the most essential principles for designing novel zeolite materials and applications. Thus, it is highly desirable to understand the moving and transforming behaviors of different small molecules in zeolitic nanopores and probe the intricate interactions between them in such delicate situations. The recently emerged integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM) holds great potential for imaging zeolite materials at an atomic resolution, since it can greatly improve electron utilization efficiency to reduce the required electron dose and is conducive to light element imaging. This Perspective focuses on the in situ observation of single-molecule adsorption−desorption behaviors in zeolites using the in situ iDPC-STEM imaging technique. We demonstrated that iDPC-STEM is an effective method for probing atomic structures of beam-sensitive zeolite materials and exhibits a remarkable ability in imaging light elements under low-dose conditions. Subsequently, we introduce a general "confined freezing" strategy to immobilize small molecules in size-matchable nanopores, which are stable enough for atomically resolved single-molecule imaging. Finally, three industrially important aromatic molecules with slight differences, including benzene, p-xylene, and pyridine, were selected to demonstrate the different adsorption/desorption behaviors and corresponding host−guest interactions at the subnanometer scale. In this way, we provide a real-space methodology to actually "see" the movement and transformation of individual molecules at the atomic scale and pave the way for clarifying the key role of host−guest interactions in molecular adsorption, diffusion, and reaction processes.