Rotacatenane is an interlocked compound composed of two mechanically interlocked macrocyclic components, i.e., a catenane, and one axle component. In this paper we describe the selective synthesis of isomeric rotacatenanes. Two rotaxanes with different phenanthroline moieties were synthesized by the oxidative coupling of an alkyne with a bulky blocking group, which proceeded in the cavity of the macrocyclic phenanthroline-Cu complex. The metal template method was used to install another cyclic component: the tetrahedral Cu(I) complex, which was composed of a rotaxane and an acyclic phenanthroline derivative, was synthesized, and the cyclization of the phenanthroline derivative gave the rotacatenane. The sequential isomers of rotacatenanes were distinguished by 1H and 13C NMR spectroscopy.