In this paper, the plane wave ultra-soft pseudopotential method was performed to analyze the effect of neutral Zn vacancy (VZnZn) and O vacancy (VOO) on the electronic and magnetic properties of Mn-doped ZnO systems. In a 2×2×22×2×2 ZnO:Mn supercell, the sites of VZnZn and VOO were set as nearest neighbor, next nearest neighbor and far nearest neighbor relative to Mn site, respectively. The results indicated that VZnZn is easier to be produced than VOO in the ZnO:Mn system, and both kinds of defects are more likely to be generated in the nearest neighbor of Mn site. Meanwhile, the ZnO:Mn-VZnZn system is p-type conductive. The farther the distance between VZnZn and Mn, the better the conductivity of the system. Contrary to VZnZn, the ZnO:Mn-VOO system is n-type conductive. The farther the distance between VOO and Mn, the worse the conductivity of the system. Furthermore, the ZnO:Mn systems containing neutral VZnZn or VOO are both likely to be in antiferromagnetic phase. However, the presence of VZnZn will enhance the possibility, while VOO will weaken it.