Exploring highly efficient catalysts for the electrochemical hydrogen evolution reaction (HER) is highly demanded in the sustainable production of hydrogen. Herein, we report a feasible strategy to create the atomic-scale dual sites in functional graphene via introducing the secondary TM dopant into the TMN 4 pre-embedded graphene, termed as TM a N 4 /TM b for simplification. According to the free energy analysis, we identify two homogenous combinations of Mn a N 4 /Mn b and Fe a N 4 /Fe b wherein the free energies of hydrogen adsorption are 0.08 and 0.04 eV for Mn a N 4 /Mn b meanwhile 0.00 and -0.01 eV for Fe a N 4 /Fe b , respectively, indicating the significant improvement in comparison with the separated components. Furthermore, the reaction barriers of H 2 O splitting are 1.62 and 1.08 for Mn a N 4 /Mn b and Fe a N 4 /Fe b , revealing the relative better proton supply of the latter under alkaline electrolyte. Furthermore, the binding energies are -6.00 and -5.71 eV for Mn a N 4 /Mn b meanwhile -6.63 and -5.70 eV for Fe a N 4 /Fe b , respectively, which substantially exceed the corresponding cohesive energies and thereby avoid the atom clustering. Therefore, the interatomic bonding of dual active sites as a chemical facilitator paves a novel route for the design of efficient catalysts at the atomic scale.