Metal-organic cages and capsules exhibit space-specific functions based on their discrete hollow structures. To acquire enzyme-like asymmetric or intricate structures, they have been modified by desymmetrization with two or more different ligands. There is a need to establish new strategies that can desymmetrize structures in a simple way using only one type of ligand, which is different from the mixed-ligand approach. In this study, a strategy was developed to form interconvertible stereoisomers using the unsymmetric macrocyclic ligand benzimidazole[3]arene. Single-crystal X-ray diffraction analysis revealed that the isomers assembled with silver tetrafluoroborate afforded a conformationally heteroleptic Ag6L4 capsule with an intricate structure. The six Ag ions in the capsule were desymmetrized, resulting in significantly different coordination geometries. Remarkably, the capsule encapsulates a single tetrafluoroborate anion via multipoint C-H···F-B hydrogen bonds in both the solid and solution states, suggesting that anions of appropriate size and shape can act as a template for the capsule formation. These results demonstrate that the use of isomerizable and unsymmetric ligands is the effectiveness of constructing highly dissymmetric supramolecular structures from a single ligand.