AbstractUnderstanding and controlling the transformations of transition metal dichalcogenides (TMDs) from amorphous precursors into two‐dimensional (2D) materials is important for guiding synthesis, directing fabrication, and tailoring functional properties. Here, the combined effects of thermal energy and electron beam irradiation are explored on the structural evolution of 2D MoS2 flakes through the thermal decomposition of a (NH4)2MoS4 precursor inside an ultrahigh vacuum (10−9 Torr) scanning transmission electron microscope (STEM). The influence of reaction temperature, growth substrate, and the initial precursor morphology on the resulting 2D MoS2 flake morphology, edge structures, and point defects are explored. Although thermal decomposition occurs extremely fast at elevated temperatures and is difficult to capture using current STEM techniques, electron beam irradiation can induce local transformations at lower temperatures, enabling direct observation and interpretation of critical growth steps including oriented attachment and transition from single‐ to multilayer structures at atomic resolution. An increase in the number of layers of the MoS2 flakes from island growth is investigated using electron beam irradiation. These findings provide insight into the growth mechanisms and factors that control the synthesis of few‐layer MoS2 flakes through thermolysis and toward the prospect of atomically precise control and growth of 2D TMDs.