Vacancies created on a surface can alter the local electronic structure, thus enabling a higher intrinsic activity for the evolution of hydrogen and oxygen. Conventional strategies for vacancy engineering, however, have a strong focus on non-metal sulfur/oxygen defects, which have often overlooked metallic vacancies. Herein, evidence is provided that cobalt vacancies can be atomically tuned to have different sizes to achieve cobalt vacancy clusters through controlling the migration of iridium single atoms. The coalescence of Co vacancy clusters at the surface of an IrCo alloy results in an increased d-band level and eventually compromises H adsorption, leading to enhanced electrocatalytic activity toward the hydrogen evolution reaction. In addition, the Co vacancy clusters can improve the electronic conductivity with respect to the oxidized Co surface, which substantially aids in strengthening the adsorption of oxygen intermediates toward an effective oxygen evolution reaction at a low overpotential. These collective effects originate from the Co vacancy cluster and specifically enable highly efficient and stable water splitting with a low total overpotential of 384 mV in alkaline media and 365 mV in an acidic environment, achieving a current density of 10 mA cm–2.