In this work, a surface engineering strategy has been developed to implant atomic Ni mostly enriched in 1 nm thickness of MoS2 nanosheets, and suppresses the segregation of undesired NiSx. Notably, this structural regulation not only creates additional edges exposed at the inert basal plane of MoS2 nanosheets, but also increases the catalytic ability of edge sites by forming dominant NiMoS phase. As such, a low overpotential of 95 mV is achieved to deliver a current density of 10 mA cm−2, which is 242 mV decrease than unmodified MoS2, together with 86.5% preservation of initial capacity after 100 h test. Theoretical calculations further identify the activated catalytic sites both in Mo-edge and S-edge, and the specific atomic configurations enable the synergistic effect to optimize the adsorption-desorption of H∗, and is responsible for the remarkably improved hydrogen evolution reaction (HER) activity.