In order to enhance the selectivity of metal nanoparticle heterogeneous catalysts, a method for the encapsulation of metal nanoparticles by crystalline nanoporous materials was designed and implemented through a wet-chemical, capping-agent-mediated encapsulation strategy. Two thermally and chemically stable metal organic frameworks (MOFs) with different aperture sizes were chosen as the crystalline nanoporous layers for metal nanoparticle (NP) encapsulation. Successful encapsulation and good catalytic performance depended on understanding and engineering the interface between the metal catalyst core and the nanoporous shell. After the synthesis of the NPs-MOF composite, their catalytic activity and selectivity were studied. Two kinds of capping agents (polymer and surfactant) were used to demonstrate different mechanisms for NP encapsulation. The polymer (polyvinylpyrrolidone, PVP) induced interaction between the NP surface and MOF precursors while the surfactant (cetyltrimethylammonium bromide, CTAB) controlled the alignment between the metal nanoparticles and MOFs. Furthermore, the capping-agent-directed overgrowth could be a general method of not only loading various inorganic nanoparticles into MOF single crystals but also bridging two porous materials with totally different structures. MOF shells were further functionalized by postsynthetic linker exchange. By applying the process, a new concept was introduced for the formation of enlarged pore apertures by linker dissociation during MOF linker exchange, as demonstrated by the postsynthetic encapsulation of species much larger than the pore aperture of the MOF structure. Kinetic studies of linker exchange rely on the competition between associative and dissociative linker exchange mechanisms. It was found that guest encapsulation was enhanced under conditions that favored the dissociative pathway. Through kinetics studies, linker exchange rate was also found to vary in different solvents. The different exchange rates were then used to create hierarchical porosity in MOF structure, and a double-solvent-mediated overgrowth strategy was designed to form hollow and mesoporous MOF. The results help to provide new ideas for nanopores related heterogeneous catalysis. The discussion of active metal NP cores with a nanoporous shell, as a frontier core-shell material, may benefit further study in developing highly selective catalysts.