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　Ru-3　clusters　anchored　on　ZIF-8　(Ru-1@ZIF-8,　Ru-3@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　Ru-3@ZIF-8　and　Ru-1@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.