Local magnetic impurities arising from atomic vacancies in two-dimensional (2D) nanosheets are predicted to have a profound effect on charge transport due to resonant scattering, and provide a handle for enhancing thermoelectric properties through the Kondo effect. However, the effects of these impurities are often masked by external fluctuations and turbostratic interfaces, therefore, it is highly challenging to probe the correlation between magnetic impurities and thermoelectric parameters experimentally. In this work, we demonstrate that by placing Molybdenum Disulfide on a hexagonal Boron Nitride substrate, a colossal spin splitting of the conduction sub-band up to ~50.0 meV is observed at the sulfur vacancies, suggesting that these are local magnetic states. Transport measurements reveal a large anomalous positive Seebeck coefficient in highly conducting n type MoS2, originating from quasiparticle resonance near the Fermi level described by the Kondo effect. Furthermore, by tuning the chemical potential, a record power factor of 50mW/mK2 in low-dimensional materials was achieved. Our work shows that defect engineering of 2D materials affords a strategy for controlling Kondo impurities and tuning thermoelectric transport.