Metallomacrocycles with internal coordination sites have a high potential to precisely control the positions of the guest ligands and the overall shape of the assemblies by utilizing the directionality and reversibility of the coordination bonds. However, when such coordinative hosts possess multiple coordination sites, it was difficult to control to which coordination sites the incoming guest ligands bind, because such systems often result in a random, uncontrolled mixture. The metallomacrocycle that we now report, a hexanuclear palladium complex of hexapap possessing six internal coordination sites, can take two different conformations depending on the guests. One is an Alternate conformation, in which six coordination sites of pap alternatively point to Up-Down-Up-Down-Up-Down. The other is a Twisted conformation, in which the coordination sites direct Up-Middle-Down-Up-Middle-Down. Interestingly, linear ditopic α,ω-diamines are captured in three distinct cross-linking modes, and regulations between the two macrocyclic conformations have been realized by the lengths of the diamines. Furthermore, the heteroleptic site-selective bridging of two kinds of diamines has been achieved. It has been demonstrated that a slight difference in the diamine lengths leads to a significant change in the structure and selection of the produced host-guest macrocyclic complexes.