This study investigates backbone engineering and evaluates the thermoelectric properties of FeCl3-doped naphthobisthiadiazole (NTz)-based donor-acceptor (D-A) conjugated polymer films. The NTz acceptor unit is coupled with three distinct donor units, namely dialkylated terthiophene (3T), dialkylated quaterthiophene (4T), and dialkylated bisthienyl thienothiophene (2T-TT) to yield copolymers designated as PNTz3T, PNTz4T, and PNTzTT. The difference in donor units leads to diverse molecule stacking and electronic properties, which can be systematically discovered via the three polymers. The linear structure of PNTz4T enables an orderly arrangement of side chains, thereby promoting dopant intercalation for enhanced carrier concentration. Additionally, this linear structure leads to an edge-on stacking mode, thereby improving the in-plane carrier mobility. As a result, the doped PNTz4T exhibits the highest electrical conductivity (σ) of 88.3 S cm-1 along with a Seebeck coefficient (S) of 62.2 µV K-1, thereby achieving the highest power factor (PF) of 34.2 µW m-1 K-2. These results highlight the relationship between the molecular design, microstructure, and doping effects in manipulating the thermoelectric performance of doped NTz-based D-A polymers.