2D crystals are attractive due to their unique atomic, electronic structures, and physiochemical properties, which strongly rely on the synthesis conditions. The atomic structure and presence of defects in the crystal lattice, such as vacancies, dopants, grain boundaries, and edge terminations, significantly influence the properties of 2D materials. Due to its high spatial resolution, aberration‐corrected scanning transmission electron microscopy (AC‐STEM) has become a powerful tool to provide atomic‐scale insights into the crystal structure, defects, heterointerfaces, ferroelectricity, and in situ observations of 2D materials. This review will cover the status of atomic‐scale studies on various 2D materials, including graphene, boron nitride, transition metal dichaogenides, MXenes, and phosphorene using AC‐STEM. The future perspective of AC‐STEM for new findings in 2D materials using machine learning is further discussed.