This paper presents a simple microfluidic method to prepare monodispersed palladium nanoparticles supported on silica/chitosan core-shell hybrid microspheres. Because a large amount of -NH2 provided by chitosan has a strong force with metal ions, Pd nanoparticles loaded on the microspheres kept monodispersed and had a mean diameter of only 2-3 nm. In addition, the core-shell structure indicating that the chitosan was mainly distributed on the shell of the microspheres results in that palladium is mainly loaded on the shell too, which can effectively reduce mass transfer distance between reactant and catalyst. Therefore, the supported Pd catalyst showed a superb catalytic performance through the hydrogenation of cydohexene. Furthermore, silica/chitosan-supported catalyst can be reused many times without an obvious loss of its activity, and it will have promising, application in other similar hydrogenation reactions.