Metal-organic frameworks (MOFs) have emerged as superior hosting matrices for atomically precise nanoclusters (NCs) encapsulation, offering excellent physical and chemical protections for advanced catalysis. Nevertheless, the MOF coating significantly reduces the NC catalytic efficiency due to the diffusion barriers and the confined microenvironments. Herein, a hierarchically engineered MOF nanoreactor was constructed by controlled structural etching for NC immobilization. This nanoreactor possesses hierarchical pores to accelerate the diffusion rate of reactants and creates hollow structures to unleash the confined NC molecules from the rigid MOF network to a capacious microenvironment. The enhanced mass transfer, improved freedom of NCs, and outstanding stability collectively boosted the catalytic activity of the nanoreactor. By controlling the etching time, freestanding Pd₈@zeolitic imidazolate framework-8 (ZIF-8)-TA₁₀ displayed a catalytic efficiency that was 3.17 times greater than that of the initial confined Pd₈@ZIF-8 and even better than free Pd₈. This work opens a new strategy to reduce the inherent limitations of porous matrixes for developing high-performance catalysts.