Poor dispersity and low stability are two predominant shortcomings hindering the applications of metal–organic polyhedra (MOPs). The confinement of MOPs in nanoscale cavities of mesoporous matrices is efficient in overcoming both shortcomings, while the improvement of the current double-solvent method is highly expected. Here we develop a facile, controllable strategy to fabricate three MOPs (coordinated from dicopper and carboxylates) in confined cavities via in situ site-induced assembly (SIA), for the first time. The cavities of mesoporous matrix SBA-16 were pre-functionalized with amine sites, which induce in situ assembly of precursors that diffused into cavities. Hence, both the amount and location of MOPs in the mesoporous matrix can be easily controlled. Upon confinement, the dispersity, stability, and catalytic performance (on ring-opening reactions) of MOPs are greatly improved. Moreover, the enhancement of stability makes it possible to observe MOPs using high-resolution transmission electron microscopy (HRTEM) directly.