One of the major challenges in heterogeneous catalysis is how to suppress the aggregation of thermodynamically unstable noble metal nanoparticles (NPs) and simultaneously maintain their high accessibility. Here we report the fabrication of integrated functional nanostructures consisting of a dendritic porous silica yolk with many small noble metal NPs and a protective mesoporous silica shell (MSS) with perpendicularly aligned pore channels and tunable shell thickness by using a well-controlled interfacial engineering strategy. Three-dimensional (3D) dendrimer-like superstructures with many permeable center-radial large pore channels and a highly accessible internal surface area, named dendritic porous silica spheres (DPSSs), serve as unique yolks not only because of their capability to accommodate high density ultrafine Au or Pt NPs, but also their functionality to act as robust physical barriers to separate and confine the aforementioned loaded NPs, which result in slowing down their aggregation at high temperatures due to Ostwald ripening. These integrated hierarchical structures also ensure good stability under weak basic and acidic conditions. Due to their superior structural properties, the DPSSs@noble metal NPs@MSS yolk-shell structures exhibit excellent catalytic performance in p-nitrophenol reduction, epoxidation reaction and CO oxidation. The favorable stability and high catalytic performance of these yolk-shell structures make the developed design strategy very useful for the fabrication of novel highly active and stable catalysts.