We studied the effect of molecular weight of a series of conjugated polymers (CPs) on the doping efficiency, electrical conductivity, and related thermoelectric properties of doped CPs. Low (L), medium (M), and high (H) molecular weight of PDFD-T polymers, based on difluorobenzothiadiazole and dithienosilole moieties, were synthesized and denoted as PDFD-T(L), PDFD-T(M), and PDFD-T(H), respectively. Furthermore, to compare the effects of different donor moieties, donor units of PDFD-T(L) were structurally modified from thiophene to thienothiophene (TT) and dithienothiophene (DTT), denoted as PDFD-TT(L) and PDFD-DTT(L), respectively. After doping the CPs with FeCl3, doped(d) PDFD-T(H) exhibited an electrical conductivity of over 400 Scm-1, which is significantly higher than those of d-PDFD-T(L), d-PDFD-T(M), d-PDFD-TT(L), and d-PDFD-DTT(L). Through various characterizations, we demonstrated that the molecular weight of CPs has a strong influence on the degree of doping and directly affects the crystallinity of the CP films and the formation of charge transporting pathways in doped films. CPs with a high molecular weight have a high carrier mobility while maintaining their original morphology and high carrier mobility even after doping. The highest power factor of >100 μWm-1K-2 was achieved through organic thermoelectric devices fabricated using PDFD-T(H). Therefore, we suggest that optimizing the molecular weight of CPs is an essential strategy for maximal power generation from their doped CP films. Overall, our work demonstrates that controlling the molecular weight of CPs can provide a key solution to minimize the crystallinity degradation of doped CPs, ultimately optimizing the doping efficiency, electrical conductivity, and thermoelectric properties.