Cyclohexanone is an important intermediate in the manufacture of polyamides in chemical industry, but direct selective hydrogenation of phenol to cyclohexanone under mild conditions is a challenge. We report here a catalyst made of Pd nanoparticles supported on a mesoporous graphitic carbon nitride, Pd@mpg-C3N4, which was shown to be highly active and promoted the selective formation of cyclohexanone under atmospheric pressure of hydrogen in aqueous media without additives. Conversion of 99% and a selectivity higher than 99% were achieved within 2 h at 65 °C. The reaction can be accelerated at higher temperature, but even at room temperature, 99% conversion and 96% selectivity could still be obtained. The generality of the Pd@mpg-C3N4 catalyst for this reaction was demonstrated by selective hydrogenation of other hydroxylated aromatic compounds with similar performance.