Abstract Minimizing disorder and defects is crucial for realizing the full potential of two-dimensional transition metal dichalcogenides (TMDs) materials and improving device performance to desired properties. However, the methods in defect control currently face challenges with overly large operational areas and a lack of precision in targeting specific defects. Therefore, we propose a new method for the precise and universal defect healing of TMD materials, integrating real-time imaging with scanning transmission electron microscopy (STEM). This method employs electron beam irradiation to stimulate the diffusion migration of surface-adsorbed adatoms on TMD materials grown by low-temperature molecular beam epitaxy (MBE), and heal defects within the diffusion range. This approach covers defect repairs ranging from zero-dimensional vacancy defects to two-dimensional grain orientation alignment, demonstrating its universality in terms of the types of samples and defects. These findings offer insights into the use of atomic-level focused electron beams at appropriate voltages in STEM for defect healing, providing valuable experience for achieving atomic-level precise fabrication of TMD materials.