Oxide-ion and proton conductors have found diverse applications such as electrolytes of solid-oxide, proton-conducting, and hybrid-ion fuel cells. Research of fuel cells with higher energy efficiency at lower operating temperature has stimulated the search for ion conductors and improved and the study of ion diffusion mechanism. Ion conduction in hexagonal perovskite-related materials is rare, and the mechanism of ion diffusion is unclear. Herein, we report high oxide-ion and proton conductivity (bulk conductivities in wet air: 11 and 2.7 mS cm−1 at 537 and 326 °C, respectively), high chemical and electrical stability in a new hexagonal perovskite-related oxide Ba7Nb3.8Mo1.2O20.1. Total direct current conductivity at 400 oC in wet air of Ba7Nb3.8Mo1.2O20.1 was 13 times higher than that of Ba7Nb4MoO20. We also report a unique dimer-mediated cooperative mechanism of the high oxide-ion conduction of Ba7Nb3.8Mo1.2O20.1 (bulk conductivities in dry air: 10 mS cm−1 at 593 °C and 1.1 mS cm−1 at 306 °C). Ab initio molecular dynamics (AIMD) simulation, neutron-diffraction experiments at 800 °C, and neutron scattering length density analyses of Ba7Nb3.8Mo1.2O20.1 indicated that the excess oxygen atoms are incorporated by the formation of both fivefold coordinated (Nb/Mo)O5 monomer and its (Nb/Mo)2O9 dimer with a corner-sharing oxygen atom and that the breaking and reforming of the dimers lead to the high oxide-ion conduction in the oxygen-deficient BaO2.1 c′ layer. The long distance between Nb/Mo and Ba cations sandwiching the c′ layer of Ba7Nb3.8Mo1.2O20.1 was found to be responsible for its low activation energy for oxide-ion conduction, leading to high conductivity at low temperatures. AIMD simulations showed that high proton conduction is attributable to proton migration in the hexagonal close-packed BaO3 layers of Ba7Nb3.8Mo1.2O20.1, which is supported by its crystal structure analysis. The present findings hold a great promise for the development and design of ion conductors.