We constructed ZnO quantum dots (QDs) with a diameter of 1.2[Formula: see text]nm of wurtzite structure, hydrogenated the surface and doped single Mn atoms using Zn-site substitution. We present an investigation of the structural and electronic properties of ZnO QDs of three doping sites: inner, intermediate and outer. Based on the density functional theory and the plane-wave pseudo potential method, the structural characteristics, charge distribution, conductivity and formation energy of doped ZnO QDs are analyzed. We obtained the effect of doping site depth on the properties above with the nearly optimal nanoparticle doping concentration (2.222%). The internal doping (inner and intermedium) configuration results in higher electrical conductivity and stronger bonds than the outer doping configuration. In particular, intermediate doping is highly efficient and valuable for obtaining Mn-doped ZnO nanoparticles with good structural and electronic properties. This study provides a theoretical reference for the survey of zero-dimensional dilute magnetic semiconductors.