Electrolysis of water to produce hydrogen (H) can solve the current energy crisis and environmental problems. However, efficient hydrogen evolution reaction (HER) catalysts are still limited to a few noble metals, thus prohibiting their broad applications. Herein, first-principles calculations were carried out to investigate the theoretical HER performances of a series of N-doped graphenes containing inexpensive single- and dual-metal atoms. Among them, MN4-gra (M = Fe, Co, Ni), homonuclear MMN6-gra, and heteronuclear M1M2N6-gra mostly exhibit low HER activities due to the weak H adsorption, and only CoN4-gra, NiNiN6-gra, and CoNiN6-gra show better ΔG *H values of 0.19, 0.15 and 0.27 eV, respectively. In contrast, low-coordinated MMN5-gra and M1M2N5-gra both have rather high HER activities. In particular, the ΔG *H values of FeNiN5-gra and CoNiN5-gra are as low as -0.04 and -0.06 eV, respectively, very close to the ideal 0 eV. Detailed analyses reveal that such high activity mainly stems from the reduced metal coordination and the synergistic effect between the two metals, which greatly enhance the adsorption ability of the active center. More interestingly, the strong H adsorption of MMN5-gra /M1M2N5-gra could enable them to further adsorb a second H atom and generate a stable HMH intermediate to yield the final product H2. Under this novel mechanism, the two-step |ΔG *H| values of FeNiN5-gra and CoNiN5-gra are all no more than 0.10 eV. Our work not only discloses the important effect of coordination regulation and site synergy on enhancing the catalytic activity but also finds a new HER path on the metal-embedded N-doped graphenes.