As the only natural and sustainable carbon source, biomass shows great potential in solving current environmental and energy problems and creating a carbon-neutral society. Selective hydrogenation is a kind of important reaction. Various unsaturated functional groups in biomass are typical targets of selective hydrogenation. Therefore, selectivity is the key index to measure the efficiency of the hydrogenation reaction. Vanillin is an important platform compound in biomass conversion. In recent years, selective hydrogenation of vanillin to biofuels and other high-value-added chemicals has received widespread attention. Because vanillin has different reducible functional groups (aldehyde group, methoxy group, and hydroxyl group), it is very important to control the selectivity of vanillin hydrogenation. Vanillyl alcohol has long-lasting sweetness and nutty aromas and is used in the food and perfume industries. 2-Methoxy-4-methylphenol (MMP) is also an important biofuel. Therefore, selective hydrogenation of vanillin to vanillyl alcohol or MMP is an important synthesis route. Here, we propose a strategy to introduce the chemical active center of catalytic reaction and the anchoring center of metal nanoparticle deposition by doping nitrogen atoms of graphene, which makes the application of graphene in hydrogenation catalysis obtain better performance. In this work, we report a simple method for in-situ synthesis of nitrogen-doped graphene-supported palladium nanoparticles Pd@N/C-2 catalyst and its application in selective hydrogenation of the C=O bond. The prepared catalyst has good catalytic activity and product selectivity for the hydrogenation of vanillin and has the advantages of simple preparation, high activity and stable performance. It is easy to be separated from organic reaction conditions and can be reused many times. Under relatively mild reaction conditions, Pd@N/C-2 catalyzed the complete conversion of vanillin to vanillyl alcohol and MMP, and the yields were 89% and 99%, respectively. It is worth noting that through the regulation of solvents, we achieved highly selective hydrogenation of vanillin to vanillyl alcohol and MMP, respectively.