Higher manganese silicide (HMS) is a promising thermoelectric (TE) semiconductor that operates effectively at medium temperatures. It is characterized by its abundance, environmental friendliness, and desirable impact resistance properties. To enhance the TE properties of HMS, this study employs isoelectronic anion and cation codoping, combined with embedded quantum dot (QD) techniques. The introduction of element doping and nanoinclusions, such as Mn0.96Re0.04(Si0.96Ge0.04)1.79+1.5%Ag2Pt QDs sample, leads to an approximately 85% increase in electrical conductivity. This boost is attributed to the adjustment of the band structure through Re, Ge, and Ag element doping and the charge transfer facilitated by MnSi, Si, and Pt precipitates. Furthermore, the enhanced PF of 1.85 × 10−3 W m−1 K−2 at 773 K is approximately 29% higher than that of pure HMS. Simultaneously, the increase in point defects hampers the improvement of lattice thermal conductivity (κl) by intensively scattering short-wave phonons. This effect is complemented by the precipitation of Si, MnSi, Ag, and Pt nanoparticles, which increases the density of grain boundaries, enhances medium-wave phonon scattering, and substantially reduces κl to 1.45 W m–l K−1 (at 773 K), ∼30% lower than that of pure HMS. The figure of merit of the sample containing 1.5%Ag2Pt QDs at 823 K attains a value of 0.69, which is ∼52% and ∼19% higher than that of pure HMS and Re-Ge-double-doped samples, respectively. The incorporation of isoelectronic codoping, along with the integration of metastable QDs, is demonstrated as an effective strategy for enhancing TE properties.