The hydrogenation of nitrogen-containing heterocyclic compounds and their derivatives to obtain the corresponding valuable products is of great practical significance. In this work, a highly active and selective Ni/NC hydrogenation catalyst was developed by utilizing melamine-modified high-specific surface carbon (NC) as a carrier for nickel nanoparticles (NPs), which showed excellent catalytic activity in the selective hydrogenation of methyl nicotinate, where the Ni/NC catalyst was first used for this reaction (selective hydrogenation of methyl nicotinate). It was found that nitrogen species on the surface of NC significantly promoted the decomposition of the nickel precursor and the high dispersion of nano-Ni, which effectively affected the agglomeration of the nickel metal, resulting in the distribution of nickel metal with a smaller particle size. In the selective hydrogenation of methyl nicotinate under mild conditions (130 °C, 3 h), the conversion of methyl nicotinate reached the optimal catalytic activity over the catalyst of 10% Ni/NC-1-M-I-300, in which the conversion of methyl nicotinate was 98.5% and the selectivity of methylpiperidine-3-carboxylate was 97.2%. After 5 recycles, the catalyst maintained a conversion of 95.4% for methyl nicotinate. The Ni/NC catalyst has good substrate adaptability in the selective hydrogenation of N-heterocyclic carboxylate, O-heterocyclic carboxylate, and aromatic carboxylate.