Abstract: Cryogenic transmission electron microscopy (cryo-TEM) brings a revolutionary breakthrough to the development of structural biology. In recent years, cryo-TEM has also been becoming an indispensable characterization method for the research of molecular materials in chemistry, especially for microstructure determination of self-assembly system in liquids, weak-bonded and electron beam-sensitive materials. The characteristic functions of cryo-TEM in Institute of Chemistry, Chinese Academy of Sciences and its applications in the research of molecular materials in chemistry were introduced, including high resolution characterization of electron beam sensitive materials, structure determination of the nano/micro crystals with the 3D electron diffraction, fine structural characterization of liquid samples, electron energy loss spectroscopy analysis, electron tomography, and single particle analysis. Combined with the new technology, the perspectives in the development of cryo-TEM in the field of chemistry were put forward.