Macrocyclic ligands have been extensively applied to recognize single metal ions with high selectivity and good affinity based on the size-match principle. The resulting metal-macrocycle complexes play a significant role in mimicking the function of natural metal ion carriers and understanding and reproducing the catalytic activity of metalloenzymes. Because of the known macrocyclic effect, those single metal-macrocycle adducts often show an enhanced kinetic and thermodynamic stability in comparison with their open-chain analogues. By virtue of such extraordinary coordination properties of macrocyclic ligands, it is expected that larger macrocycles with multiple coordination sites could properly act as an outer scaffold to direct the formation of multiatom species inside, such as polynuclear metal cluster aggregates, whose assembly may largely depend on the template positioning of coordinative atoms in the macrocyclic ring. Thus, the employment of polydentate macrocyclic ligands may provide a convenient tool to access polynuclear metal clusters in a controllable way. In this Account, we review our studies of the metal ion binding process of a class of polydentate macrocyclic ligands, azacalixpyridines (Py[ n]s), and the application of Py[ n]s as an outer template to direct the controllable synthesis of polynuclear metal clusters. Our investigations revealed that Py[ n]s show a significant cooperative coordination effect in the metal ion binding process that facilitated the easy formation of a polymetallic assembled structure. Taking advantage of the cooperative coordination effect and the tunable and highly fluxional conformation of Py[ n]s, we laid our focus on control of the nuclearity number by tuning the size of Py[ n]s and the adoption of Py[ n]s with different anionic centers in metal cluster synthesis. As an important example for application, this new established macrocycle-directed method has been employed to achieve a variety of metal-cluster-centered capsule, rotaxane, catenane, polygon, and other supramolecular assemblies. Furthermore, a cluster-to-cluster transformation inside the cavity of Py[ n]s is presented to showcase the use of the acquired metal cluster-macrocycle complexes to achieve unconventional metal cluster entities. With regard to the application of the newly synthesized macrocycle-encircled metal clusters, examples of the fabrication of functional materials and catalysts are presented. With the assistance of Py[ n]s, a bulk-to-cluster-to-nanoparticle transformation of silver sulfide (Ag2S) and silver halides (AgX) has been conducted to produce a series of nonstoichiometric silver sulfide and halide nanoparticles. The resulting Ag-S nanoparticle material with a high Ag/S ratio, which is inherited from the Py[ n]-protected polysilver sulfide clusters, has a large energy gap relative to conventional Ag2S nanoparticles. Moreover, the nonstoichiometric silver halide nanoparticles can act as a new kind of electrocatalyst for the chlorine evolution reaction, showing excellent selectivity and high catalytic efficiency. Overall, in this Account we try to highlight the application of polydentate macrocycles as an outer template to guide the synthesis of polynuclear metal clusters in a controllable manner. This unique synthesis will provide a new avenue to access unconventional metal clusters of different metal kinds and diverse anionic centers, which are expected to have promising and significant applications in many interdisciplinary areas of chemistry.