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