Abstract2D transition metal dichalcogenides (TMDs) exhibit remarkable properties that are strongly influenced by their atomic structures, as well as by various types of defects and interfaces that can be precisely engineered and controlled. These features make 2D TMDs and TMD‐based materials highly promising for a wide range of applications in electronics, optoelectronics, magnetism, spintronics, catalysis, energy, etc. By providing a comprehensive approach to understand the structure–property–functionality relationship in materials at the atomic scale, electron microscopy, and spectroscopy techniques have emerged as invaluable tools for studying both the static characteristics and dynamic evolutions of 2D TMDs. In this review, the primary focus lies in exploring intrinsic and artificial structures in TMDs and their heterostructures, along with their corresponding properties, through cutting‐edge aberration‐corrected scanning transmission electron microscopy (STEM) and electron energy loss spectroscopy (EELS). Additionally, recent advancements in the field of in situ visualization and manipulation of 2D TMDs using electron beams are highlighted. It is anticipated that the up‐to‐date overview provided, along with a glimpse into the future development of STEM‐based techniques, will make a substantial contribution to advancing research on 2D materials.