The synthesis of supramolecular compounds with a high degree of controllability and the targeted modulation of their topological transitions pose significant challenges in situ. In this study, we have successfully constructed an array of discrete structures based on a series of bidentate pyridyl ligands (L1, L2, and L3), which were subsequently ligated with half‐sandwiched (Cp*Ir fragments) building blocks. Our further investigations elucidate a strategy for coordinating the relative lengths of the bidentate ligands with the building blocks, achieving specific concentrations that drive the transformation of tetranuclear metal macrocycles into Borromean rings. Notably, the distinct characteristics of the three pyridyl ligands markedly influence the efficiency of synthesis and the topological conversion of the supramolecular macrocycles. Detailed structural analyses reveal that π‐π stacking interactions, the electron‐donating capabilities of the ligands, and hydrogen‐bonding interactions are pivotal in stabilizing these molecular macrocycles and in facilitating their transformation to Borromean rings. The analyses underscore the importance of the electron‐rich effect induced by the sulfur atoms in the ligands and the regulation and modulation of the pyridine functional group in contributing to the structural stability and altered characteristics of the macrocycles.