Here we report a novel approach to synthesize atomically dispersed uniform clusters via a cage-separated precursor preselection and pyrolysis strategy. To illustrate this strategy, well-defined Ru-3(CO)(12) was separated as a precursor by suitable molecular-scale cages of zeolitic imidazolate frameworks (ZIFs). After thermal treatment under confinement in the cages, uniform Ru-3 dusters stabilized by nitrogen species (Ru-3/CN) were obtained. Importantly, we found that Ru-3/CN exhibits excellent catalytic activity (100% conversion), high chemoselectivity (100% for 2-aminobenzaldehyde), and significantly high turnover frequency (TOF) for oxidation of 2-aminobenzyl alcohol. The TOF of Ru-3/CN (4320 h(-1)) is about 23 times higher than that of small-sized (ca. 2.5 nm) Ru particles (TOF = 184 h(-1)). This striking difference is attributed to a disparity in the interaction between Ru species and adsorbed reactants.