Incorporating atomically dispersed metal species into functionalized metal–organic frameworks (MOFs) can integrate their respective merits for catalysis. A cage‐controlled encapsulation and reduction strategy is used to fabricate single Ru atoms and triatomic Ru3 clusters anchored on ZIF‐8 (Ru1@ZIF‐8, Ru3@ZIF‐8). The highly efficient and selective catalysis for semi‐hydrogenation of alkyne is observed. The excellent activity derives from high atom‐efficiency of atomically dispersed Ru active sites and hydrogen enrichment by the ZIF‐8 shell. Meanwhile, ZIF‐8 shell serves as a novel molecular sieve for olefins to achieve absolute regioselectivity of catalyzing terminal alkynes but not internal alkynes. Moreover, the size‐dependent performance between Ru3@ZIF‐8 and Ru1@ZIF‐8 is detected in experiment and understood by quantum‐chemical calculations, demonstrating a new and promising approach to optimize catalysts by controlling the number of atoms.