Metal clusters (MCs) with dimensions between a single metal atom and nanoparticles of >2 nm usually possess distinct geometric and electronic structures, their outstanding performance in catalysis applications have underpinned a broad research interest. However, smaller-sized MCs are easily deactivated by migration coalescence during the catalysis process because of their high surface energy. Therefore, the search of an appropriate stabilizer for MCs is urgently demanded. In recent years, porous organic polymers (POPs) and organic molecular cages (OMCs), as emerging functional materials, have attracted significant attention. Benefiting from the spatial confinement, encapsulating MCs into these porous organic materials is a promising approach to guarantee the uniform size distribution and stability. In this review, we aim to provide a comprehensive summary of the recent progress in the synthetic strategies and catalysis applications of the encapsulated MCs, and seek to uncover promising ideas that can stimulate future developments at both the fundamental and applied levels.