Using the first-principles calculations based on the density functional theory, we have investigated the magnetic properties of Cu-doped ZnO both in bulk and nanocluster. The calculated results show that the substitutional Cu ions are spin polarized and have a tendency to assemble. It is found that the ground state has shown a change from ferromagnetic phase to antiferromagnetic phase as the size for the doping system decreases from bulk to nanocluster. In bulk ZnO, the ferromagnetism is attributed to the strong hybridization between Cu 3d and O 2p states. In ZnO nanocluster, however, the antiferromagnetic exchange interaction is dominant because of the very close Cu–Cu distance. ► The Cu ions are spin polarized and have a tendency to assemble. ► Intrinsic defects have a large effect on the ground-state magnetic ordering. ► The magnetic phase is different for different sizes of the doping system.