The effect of 3d transition-metal (TM) atoms (Sc–Ni) substitutional doping on the structural, electronic and magnetic characters of PC6 ([email protected]6) is systemically investigated by first-principles calculations in the framework of density functional theory. Our calculations show that introducing of V, Cr, Mn and Fe atoms makes the original non-magnetic PC6 changing into ferro-magnetic, while Sc, Ti, Co and Ni atoms substitutional doped PC6 are still non-magnetic. The magnetic behavior can be qualitatively interpreted by a simple model, which associated with hybridization between the 3d orbitals of TM atoms and the defect levels of unrelaxed D3h symmetrical P vacancy, i.e., hybridization model. The occupation of electrons in hybridized electronic levels determines whether the doping system is magnetic: when the bonding levels (for [email protected]6 and [email protected]6), the nonbonding levels and antibonding levels (for [email protected]6 and [email protected]6) are fully occupied, the corresponding doping systems have no magnetic, while when the nonbonding levels and the antibonding levels (for [email protected]6, [email protected]6, [email protected]6 and [email protected]6) become partially filled, these systems exhibit localized spin moments of 1–3 μB. The results are helpful to understand the origin of magnetism in [email protected]6 and provide a theoretical basis for potential applications in spintronic devices.