Silica hollow microspheres with moonscape-like rough surface (RS) and macroporous surface (MS) have been controllably synthesized by a water-oil-water three-phase emulsion method, which are used as supports of the heterogeneous catalysts for the catalytic hydrogenation of nitrile-butadiene rubber (NBR). It is found that Pd can be uniformly dispersed on both amino-functionalized RS and MS supports and both the catalysts show high hydrogenation activity with 100% selectivity to C=C bonds. However, the reusability of Pd/N-RS is much better than that of Pd/N-MS, maintaining 92% of activity without any regeneration treatment after five times of recycling experiment. The high activity retention is because the moonscape-like surface of the RS support is favorable for the contact of NBR macromolecules with the active sites, and more importantly, the NBR macromolecules do not need to diffuse into the interior of the catalyst, leading to fast desorption of the hydrogenated NBR from the surface of catalyst and re-exposure of the active sites.