Carbon nanotube (CNTs) and activated carbon (AC) supported Pd and Ni catalysts were prepared for the (in situ) hydrogenation of phenol to cyclohexanone and cyclohexanol. The hydrophobic/hydrophilic properties of the catalysts were tailored by pretreating the carbonaceous support with HNO3 at various conditions and characterized by X-ray photoelectron spectroscopy (XPS), temperature-programmed desorption (TPD), and transmission electron microscopy (TEM). The catalytic results suggested that Pd and Ni supported on CNTs show significantly higher activity than that supported on ACs. Pretreating the CNTs with HNO3 increases the local hydrophilicity of the active phase (by introducing oxygenated groups), which result in an increase in the cyclohexanone selectivity and strongly decrease the phenol conversion. The first-principles density functional theory calculation suggested that the adsorption/desorption behaviors of phenol, methanol, H2O, and cyclohexanone on the catalysts might be influenced highly by the hydrophobic/hydrophilic properties. The hydrophilic catalysts show high selectivity in cyclohexanone by lower conversion in phenol or vice versa.