Understanding the electronic structure of doped InP quantum dots (QDs) is essential to optimize the material for specific optoelectronic applications. However, current synthesis approaches are often tedious and unfavorable for rational tunning. Herein, a combination of experimental and computational studies was conducted to address the doping mechanism and surface passivation of InP QDs. The successful dopant introduction requires low Cu doping concentration and heavy Mn doping, while the Ag doping amount is relatively moderate. This may correspond to the theoretical doping formation energy presented as Cu (−2.52 eV) < Ag (−1.76 eV) < Mn (−0.38 eV). As for surface passivation, inorganic ions and shell-like ZnS are unraveled through simulational investigation. Chloride ion promotes oriented growth toward tetrahedron morphology while nitrate-passivated InP QDs exhibit blurry transmission electron microscope (TEM) morphology. Correspondingly, the binding energy of chloride ion with (111) facet is −2.13 eV significantly lower than those of ( 110) and (100) facets. Further, the additional Zn 3d bands are more involved in the formation of conduction band, which optimized the Mn-doped InP with a 0.32 eV bandgap. These experimental and model results provide more microscopic details of doped InP, which can motivate theoretically exact control of guest ion stoichiometry with optimized characteristics for electrical devices.