AbstractMimicking the structures and functions of cells to create artificial organelles has spurred the development of efficient strategies for production of hollow nanoreactors with biomimetic catalytic functions. However, such structure are challenging to fabricate and are thus rarely reported. We report the design of hollow nanoreactors with hollow multishelled structure (HoMS) and spatially loaded metal nanoparticles. Starting from a molecular‐level design strategy, well‐defined hollow multishelled structure phenolic resins (HoMS‐PR) and carbon (HoMS‐C) submicron particles were accurately constructed. HoMS‐C serves as an excellent, versatile platform, owing to its tunable properties with tailored functional sites for achieving precise spatial location of metal nanoparticles, internally encapsulated (Pd@HoMS‐C) or externally supported (Pd/HoMS‐C). Impressively, the combination of the delicate nanoarchitecture and spatially loaded metal nanoparticles endow the pair of nanoreactors with size–shape‐selective molecular recognition properties in catalytic semihydrogenation, including high activity and selectivity of Pd@HoMS‐C for small aliphatic substrates and Pd/HoMS‐C for large aromatic substrates. Theoretical calculations provide insight into the pair of nanoreactors with distinct behaviors due to the differences in energy barrier of substrate adsorption. This work provides guidance on the rational design and accurate construction of hollow nanoreactors with precisely located active sites and a finely modulated microenvironment by mimicking the functions of cells.