Atomic-scale charge-transport properties of Au-Ag ion clusters aligned as wires in host molecular cages were measured by a scanning tunneling microscopy-based break junction method. The Au-Ag ion wires were prepared by doping guest Ag ions into Au ion wires through a self-assembly process. We demonstrated that the electronic conductance of the Au ion wires can be modulated by 10 times by doping the guest Ag ion based on statistical analysis of the electronic investigations.