Understanding the source of magnetism in Mn doped ZnO (ZnO:Mn) is an active area of research, made difficult experimentally by the challenge of controlling point vacancies in ZnO:Mn. Therefore, the stability and magnetic properties of ZnO:Mn with point vacancies were studied by first-principles calculations based on density functional theory (DFT). Formation energy and magnetic moment calculation results show that Mn prefers to cluster in ZnO:Mn. This clustering can become uniformly distributed through modifications by Zn vacancies (V Zn ) or O vacancies (Vo). Magnetic analysis shows that Mn dopant in Zn site (ZnO:Mn Zn ) coupled with V Zn or interstitial Mn (Mn i ) coupled with V O makes ZnO having long-range ordered ferromagnetism (FM) and an increased Curie temperature ( Tc ) above room-temperature. The ZnO:Mn Zn with V Zn exhibits obvious half-metallic characteristics that are of essential benefit to the design and preparation of a new-type of spin-electron injection source dilute magnetic semiconductor. The magnetic sources of ZnO:Mn Zn with V Zn and Mn i -doped ZnO (ZnO:Mn i ) with V O arise from carrier-mediated magnetic interaction and the double exchange of Mn3d, O2p and Zn4s orbitals, consistent with the theories of average field approximation and the double exchange mechanism.