New π-conjugated polymers with strong electron affinity, PNDTI-BBTs, consisting of naphtho[2,3-b:6,7-b′]dithiophenediimide (NDTI) and benzo[1,2-c:4,5-c′]bis[1,2,5]thiadiazole (BBT) units, were synthesized. PNDTI-BBTs have low-lying LUMO energy levels (∼−4.4 eV), which is sufficiently low for air-stable electron transport in organic field-effect transistors and for being readily doped by a well-known n-dopant, N,N-dimethyl-2-phenyl-2,3-dihydro-1H-benzoimidazole (N-DMBI), affording doped polymer films with relatively high conductivities and Seebeck coefficients. Depending on the solubilizing alkyl groups (2-decyltetradecyl, PNDTI-BBT-DT, or 3-decylpentadecyl groups, PNDTI-BBT-DP), not only the electron mobility in the transistor devices with the pristine polymer thin films (PNDTI-BBT-DT: ∼0.096 cm2 V-1 s-1; PNDTI-BBT-DP: ∼0.31 cm2 V-1 s-1) but also the conductivity and power factor of the doped thins films (PNDTI-BBT-DT: ∼0.18 S cm-1 and ∼0.6 μW m-1 K-2; PNDTI-BBT-DP: ∼5.0 S cm-1 and ∼14 μW m-1 K-2) were drastically changed. The differences in the electric properties were primarily ascribed to the better crystalline nature of the PNDTI-BBT-DP than those of PNDTI-BBT-DT in the thin-film state. Furthermore, UV-vis and ESR spectra demonstrated that doping effectiveness was largely affected by the alkyl groups: the PNDTI-BBT-DP films with better crystalline order prevented overdoping, resulting in ca. 20 times higher conductivity and power factors. From these results, it can be concluded that tuning the intermolecular interaction and consequently obtaining the thin-film with well-ordered polymers by the alkyl side chains is a promising strategy for developing superior thermoelectric materials.