A catalysis/membrane filtration system combining a catalytic reaction and a separation process can realize the in situ separation of ultrafine catalysts from the reaction mixture and make the production continuous. In this study, a side-stream catalysis/membrane filtration system was developed for the first time for the continuous liquid-phase hydrogenation of phenol over Pd@CN to produce cyclohexanone. The operating parameters including the reaction and filtration conditions were optimized by balancing their influences on the catalytic and separation properties. It was found that the properties Of the side-stream catalysis/membrane filtration system depended strongly on the operating Conditions. Continuous phenol hydrogenation over Pd@CN was performed under the optimized operating conditions. A stable operation of 30 h was achieved with both a phenol conversion and a cyclohexanone selectivity of greater than 85%, and the ceramic membrane showed excellent stability. This study is a contribution to the development of green cyclohexanone production processes.