Direct observation of atomic migration both on and below surfaces is a long-standing but important challenge in materials science as diffusion is one of the most elementary processes essential to many vital material behaviors. Probing the kinetic pathways, including metastable or even transition states involved down to atomic scale, holds the key to the underlying physical mechanisms. Here, we applied aberration-corrected transmission electron microscopy (TEM) to demonstrate direct atomic-scale imaging and quasi-real-time tracking of diffusion of Mo adatoms and vacancies in monolayer MoS2, an important two-dimensional transition metal dichalcogenide (TMD) system. Preferred kinetic pathways and the migration potential-energy landscape are determined experimentally and confirmed theoretically. The resulting three-dimensional knowledge of the atomic configuration evolution reveals the different microscopic mechanisms responsible for the contrasting intrinsic diffusion rates for Mo adatoms and vacancies. The new insight will benefit our understanding of material processes such as phase transformation and heterogeneous catalysis.