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Precisely regulating the electronic structures of metal active species is highly desirable for electrocatalysis. However, carbon with inert surface provide weak metal-support interaction, which is insufficient to modulate the electronic structures of metal nanoparticles. Herein, we propose a new method to control the electrocatalytic behavior of supported metal nanoparticles by dispersing single metal atoms on an O-doped graphene. Ideal atomic metal species are firstly computationally screened. We then verify this concept by deposition of Ru nanoparticles onto an O-doped graphene decorated with single metal atoms (e.g., Fe, Co, and Ni) for hydrogen evolution reaction (HER). Consistent with theoretical predictions, such hybrid catalysts show outstanding HER performance, much superior to other reported electrocatalysts such as the state-of-the-art Pt/C. This work offers a new strategy for modulating the activity and stability of metal nanoparticles for electrocatalysis processes.