Abstract: Transmission electron microscopy (TEM), having a remarkably high spatial resolution and diversified analysis capability, can be used to obtain very comprehensive composition, structure, and crystal chemistry of the samples under submicron-nanometer scale and is a powerful tool for studying the microscopic components and structure of geological samples. It has been applied increasingly in earth science, including mineral deposits. In this paper, TEM is used as an example of studying rare earth deposits. Firstly, we briefly introduce the TEM’s fundamental structure, working principles, function, and sample preparation method. Then, we review the application of TEM in the study of rare earth element (REE) deposits from carbonatite-, pegmatite-, granitoid weathering crust-, and phosphorite- to deep-sea sediment types. The work involves the bastnaesite’s growth mechanism of crystallization of particle attachment, the apatite and zircon’s dissolution, migration, and re-precipitation during hydrothermal metasomatism, the microstructure of primary REEs and the mineral types of weathering products in the granitoid weathering crust deposits, the apatite’s occurrence state and substitution mechanism of trace REEs at the nano to atom scale. Finally, the cautions and application prospects for the TEM in studying geology in the future are summarized.