Abstract Achieving high thermoelectric performance in conjugated polymers is challenging because chemical doping perturbs the microstructure and induces electronic disorder, limiting the simultaneous enhancement of electrical conductivity ( σ ) and the Seebeck coefficient ( S ). Herein, a rational molecular design strategy is proposed for diketopyrrolopyrrole (DPP)‐based conjugated polymers that combines an asymmetric side‐chain configuration—a branched alkyl group on one side and a polar oligo(ethylene glycol) (OEG) group on the other—with electron‐rich donor units (thiophene, thienothiophene, and bithiophene). These structural modifications modulate energy levels, dopant miscibility, and interchain interactions, facilitating higher doping levels and favorable molecular packing for charge transport. However, doped microstructures exhibit pronounced sensitivity to the specific combination of oxygenated side chains and donor units, with increasing doping levels leading to molecular disorder or abnormal doping behavior. Among the series, PODEGT—comprising a monothiophene donor and an asymmetric OEG side chain—achieved an optimal balance between doping efficiency and structural order, thereby enabling concurrent improvements in σ and S and yielding an exceptional power factor of 561.9 µW m −1 K −2 , the highest reported for DPP‐based conjugated polymers. These results establish a generalizable molecular design strategy that reconciles doping efficiency with microstructural robustness, providing a breakthrough toward high‐performance organic thermoelectrics.