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Luminescent materials are indispensable for applications in lighting, displays and photovoltaics, which can transfer, absorb, store and utilize light energy. Their performance is closely related with their size and morphologies, exact atomic arrangement, and local configuration about photofunctional centers. Advanced electron microscopy‐based techniques have enabled the possibility to study nanostructures with atomic resolution. Especially, with the advanced micro‐electro‐mechanical systems, it is able to characterize the luminescent materials at the atomic scale under various environments, providing a deep understanding of the luminescent mechanism. Accordingly, this review summarizes the recent achievements of microscopic study to directly image the microstructure and local environment of activators in lanthanide and manganese (Ln/Mn2+)‐doped luminescent materials, including: 1) bulk materials, the typical systems are nitride/oxynitride phosphors; and 2) nanomaterials, such as nanocrystals (hexagonal‐phase NaLnF4 and perovskite) and 2D nanosheets (Ca2Ta3O10 and MoS2). Finally, the challenges and limitations are highlighted, and some possible solutions to facilitate the developments of advanced luminescent materials are provided.