Cyclohexanone is significant chemical reagent for organic synthesis, so it is key to design and prepare a highly active and environmentally friendly catalyst for the conversion of phenol to cyclohexanone. The results in this work show that the Pd-based supported nanocatalysts (Pd/SiO2) with various Pd contents (Pd/SiO2–1 with 0.16 wt% Pd, Pd/SiO2–2 with 0.26 wt% Pd, Pd/SiO2–3 with 0.52 wt% Pd, Pd/SiO2–4 with 2.60 wt% Pd) have high conversion and selectivity in phenol selective hydrogenation to cyclohexanone under relatively moderate reaction parameters, Pd/SiO2–2 with the highest conversion of 80.6%, selectivity of 92.1% and turnover frequency (TOF) of 1106.1 h−1. This excellent activity is attributed to the highly dispersed Pd nanoparticles (NPs) on silica with high surface area. The Pd/SiO2 catalysts are with high Pd dispersion and strong interaction of Pd-SiO2, which have been proved by XRD, XPS, BET, TEM, HRTEM, STEM, STEM-EDS elemental analysis techniques. The as-prepared materials have good catalytic behaviors in the selective hydrogenation of phenol and good stability, facilitating phenol hydrogenation to cyclohexanone and preventing the excessive hydrogenation of cyclohexanone to cyclohexanol.