Developing a new strategy to mitigate the trade-off between the Seebeck coefficient, electrical conductivity, and thermal conductivity is of great importance for designing highly efficient thermoelectric (TE) materials. Recently, utilizing magnetism or spin degree-of-freedom has attracted interest as an effective way to overcome such a trade-off. Here, an unprecedented pathway to enhance the Seebeck coefficient is proposed in a magnetic-impurity-doped half metal by virtue of a novel “spin polarization relaxation” mechanism. Using Fe/Co-doped higher-manganese silicides (HMSs) as a platform, it is shown that alteration of the magnetic structure and accompanying modification of the spin-dependent band structure can lead to a significantly improved Seebeck coefficient. Magnetic characterization suggests that extrinsic Fe/Co ions are antiferromagnetically coupled with intrinsic Mn ions, reducing the magnetic moment of the doped HMS. Spin-polarized density functional theory calculations disclose that such antiferromagnetic coupling leads to magnetization-induced band shifts and thus the relaxed spin polarization of density-of-states at the Fermi level. Based on those calculation results, a two-spin-channel transport model is developed to explain the relationship between the relaxed spin polarization and the drastic increase of the Seebeck coefficient in the doped HMS. Our study opens up new TE research opportunities in various spin-polarized systems such as half metals which have seldom been investigated so far.