Mechanical properties of metallic glasses depend on their microstructure. Rejuvenation recently has attracted much attention because it is a potential tool for controlling the microstructure and properties of metallic glasses. Here I explain molecular dynamics studies on microstructure control and deformation behaviors of metallic glasses. From atomistic simulation approaches, I revealed the thermal rejuvenation process in the heterogeneous microstructure of metallic glasses, the formation of nanocrystals in thermal processing for rejuvenation, and the effects of rejuvenation and nanocrystallization on deformation behaviors.