Integrated differential phase‐contrast scanning transmission electron microscopy (iDPC‐STEM) is capable of directly probing guest molecules in zeolites, owing to its sufficient and interpretable image contrast for both heavy and light elements under low‐dose conditions. This unique ability is demonstrated by imaging volatile organic compounds adsorbed in zeolite Silicalite‐1; iDPC‐STEM was then used to investigate molybdenum supported on various zeolites including Silicalite‐1, ZSM‐5, and mordenite. Isolated single‐Mo clusters were observed in the micropores of ZSM‐5, demonstrating the crucial role of framework Al in driving Mo atomically dispersed into the micropores. Importantly, the specific one‐to‐one Mo‐Al interaction makes it possible to locate Al atoms, that is, catalytic active sites, in the ZSM‐5 framework from the images, according to the positions of Mo atoms in the micropores.