Although the nickel-based catalyst is able to exhibit comparative catalytic activity to noble metal for methyl acrylate hydrogenation, it requires strict reaction condition, which can be improved by regulation of coordination environment. In this study, we constructed a kind of Ni single-atom coordinated with N and S (Ni-NSC) through the pyrolysis of organic Ni-based precursors at 600 °C. The existence and fine structure of Ni single-atom were confirmed by the spherical electron microscopic observation in combination with the X-ray absorption spectroscopy (XAS) characterization. In addition, the catalytic hydrogenation assessment suggested that the as-prepared Ni-NSC catalyst exhibited higher activity and stability than the Ni/NSC supported catalyst prepared by incipient wetness impregnation method. This remarkable catalytic activity was due to the high dispersion and density of Ni single-atom and weak adsorption energy of intermediates on these Ni sites.