Unipolar n‐type semiconducting polymers based on the benzobisthiadiazole (BBT) unit and its heteroatom‐substituted derivatives are for the first time synthesized by the D‐A1‐D‐A2 polymer‐backbone design strategy. Selenium (Se) substitution is a very effective molecular design, but it has been seldom studied in n‐type polymers. In this study, within the similar conjugated framework, the Se substitution effects on the optical, electrochemical, solid‐state polymer packing, electron mobility, and air‐stability of the target unipolar n‐type polymers are unraveled. Replacing the sulfur (S) atom in the thiadiazole heterocycles with the Se atom leads to narrower bandgaps and deeper lowest unoccupied molecular orbital (LUMO) levels of the n‐type polymers. Furthermore, the Se‐substituted polymer (pSeN‐NDI) shows shorter lamellar packing distances and stronger edge‐on π–π stacking interactions than its S‐counterpart (pSN‐NDI), as observed by the two‐dimensional grazing‐incidence wide‐angle X‐ray scattering (GIWAXS) patterns. With the deeper LUMO level and thin‐film microstructures suitable for transistors, pSeN‐NDI exhibits four‐fold higher electron mobilities (μe) than pSN‐NDI. However, the other Se‐containing polymer, pSeS‐NDI, forms rather amorphous film structures, which is caused by its limited thermal stability and decomposition during the thermal annealing processes, thus giving rise to a lower μe than its S‐counterpart (pBBT‐NDI). Most importantly, pBBT‐NDI demonstrates an electron mobility of 0.039 cm2 V−1 s−1, which is noticeable among the unipolar n‐type polymers based on the BBT and its analogs.