The β-relaxation, which is the source of the dynamics in glass state and has practical significance to relaxation and mechanical properties of glasses, has been an open question for decades. Here, we propose a flow unit perspective to explain the structural origin and evolution of β-relaxation based on experimentally obtained energy distribution of flow units using stress relaxation method under isothermal and linear heating modes. Through the molecular dynamics simulations, we creatively design various artificial metallic glass systems and build a direct relation between β-relaxation behavior and features of flow units. Our results demonstrate that the β-relaxation in metallic glasses originates from flow units and is modulated by the energy distribution of flow units, and the density and distribution of flow units can effectively regulate the β-relaxation behavior. The results provide a better understanding of the structural origin of β-relaxation and also afford a method for designing metallic glasses with obvious β-relaxation and better mechanical properties.