Directional processing of metal-organic frameworks (MOFs) into unique hybrid materials with desired structures and properties is a key scientific challenge in exploring the enhanced functionality and potential applications of MOF compounds. Here, the reducibility of MOF clusters is first revealed via theoretical calculations from the viewpoint of the reduction potential energy (Ereduction), which serves as the basic principle for the site-directed reduction processing of MOFs. During this process, the active component with a high Ereduction in bimetallic MOFs is selectively reduced to metal nanostructures, while the other (inert) parts maintain their structural integrity. A series of hierarchical MOFs/metal nanoparticle composites with different structures, including yolk-shell, core-shell, and dispersed, have been successfully customized. More importantly, the as-prepared hybrid materials ([email protected]) exhibit unique size-selective properties in catalyzing ketone hydrogenation, which originate from the combination of the high catalytic performance of the nanoscale metal catalysts and the molecular sieving behavior of the MOFs' well-defined microporous nature.