Direct consideration for both, the catalytically active species and the host materials provides highly efficient strategies for the architecture design of nanostructured catalysts. The conventional wet chemical methods have limitations in achieving such unique layer-by-layer design possessing one body framework with many catalyst parts. Herein, an innovative physical method is presented that allows the well-regulated architecture design for an array of functional nanocatalysts as exemplified by layer-by-layer adornment of Pd nanoparticles (NPs) on the highly arrayed silica nanorods. This spatially confined catalyst exhibits excellent efficiency for the hydrogenation of nitroarenes and widely deployed Suzuki cross-coupling reactions; their facile separation from the reaction mixtures is easily accomplished due to the monolithic structure. The generality of this method for the introduction of other metal source has also been demonstrated with Au NPs. This pioneering effort highlights the feasibility of physically controlled architecture design of nanostructured catalysts which may stimulate further studies in the general domain of the heterogeneous catalytic transformations.