Fabrication and modification of few-atom metal clusters and even single atoms in the pores of porous materials for catalysis are highly desired from an atom-efficiency aspect but remain a great challenge. Herein, we propose a facile and efficient strategy for the encapsulation of C-N-decorated Pd sub-nanoclusters (MSNCs)/single atoms (SAs) into MOFs by the confined thermolysis of Pd-based metal-organic polyhedra (MOPs) in MOF pores. The obtained hybrids contained both Pd MSNCs (∼0.8 nm) and Pd SAs, which were stabilized by the in situ formed C-N fragments and the confinement effect of MOF pores. Benefiting from the highly exposed Pd atoms and synergistic effect between Pd and C-N fragments, these catalysts exhibited extremely high catalytic activity and stability in various important chemical processes, making them comparable to the most active Pd-based catalysts reported in the literature even under milder reaction conditions. Considering the high tunability of MOPs, this proposed strategy might provide a new toolbox for enriching the family of decorated MSNC/SA catalysts.