Metal nanoparticles (M NPs) sometimes suffer from low stability and high aggregation, reducing their reactivity during catalytic cycles. In order to obtain stable and ultrafine noble metal (Ru/Rh/Pd) and first-row transitionmetal (Co/Ni/Cu) nanoclusters, several porous coordination cages (PCCs) were applied to confine the nanoparticles within their cavities. Because of the electrostatic attraction, metal cations were only encapsulated by PCC-2a with a highly negatively charged cavity. By in situ reduction, M NPs were synthesized within the cavity of PCC-2a to form stable, ultrafine, and highly active catalyst composite. Through characterization by high resolution transmission electron microscope, the synthesized M NPs were found in face-cubic-centered single crystal form, which were rarely reported. In contrast, cages with only 6- negative charges (PCC-2b) or 12+ positive charges (PCC-3) were unable to obtain high crystalline, ultra-small M NPs, resulting in aggregation and large particle size. Finally, the M NPs@PCC catalysts exhibit different activities in methanolysis and hydrolysis of ammonium borane.