The one-step hydrogenation of phenol to cyclohexanone is green and sustainable. In this study, the effect of a CN (N-doped carbon) precursor separation mode on the catalytic performance of a Pd@CN catalyst for selective hydrogenation of phenol to cyclohexanone in water was investigated. Three modes, i.e., rotary evaporation, centrifugation, and filtration, were designed to separate the CN precursor while preparing the Pd@CN catalyst. The results highlight that the separation mode significantly affects the phenol hydrogenation performance of the Pd@CN catalyst. The best catalytic performance is obtained when separating the CN precursor by the rotary evaporation mode. Based on a series of characterizations, it is confirmed that the separation mode of rotary evaporation can introduce more N into the mesoporous carbon, improve the Pd dispersion, and enhance the basic sites and Pd loading, leading to higher catalytic activity. Furthermore, the Pd@CN catalyst prepared by rotary evaporation exhibits better catalytic stability. Less Pd leaching is responsible for its slight deactivation. These findings can provide a point of reference for the development of Pd@CN catalysts with high catalytic performance.