Three donor‐π‐acceptor (D‐π‐A) type alternating conjugated polymers, namely PIDTT‐DTNT‐C16, PIDTT‐DTNT‐HD and PIDTT‐DTNT‐OD bearing the same backbone of indacenodithieno[3,2‐b]thiophene (IDTT) as the D unit and naphtho[1,2‐c:5,6‐c′]bis[1,2,5]thiadiazole (NT) as the A moiety but with different flexible side chain (n‐hexadecyl (C16), 2‐hexyldecyl (HD) and 2‐octyldodecyl (OD)) substituted thiophene employed as π‐bridges, were synthesized and characterized. The effects of the side chain on absorption, photostability, energy levels, aggregation, backbone conformation, morphology and photovoltaic properties were systematically investigated. Because moderate D and strong A units were selected to construct the polymer backbone, a medium optical bandgap (ca. 1.66 eV) and low‐lying highest occupied molecular orbital energy level (EHOMO ≈ −5.36 V), thus resulting in a relatively higher open‐circuit voltage (VOC) of 0.80–0.83 V, were achieved. It was found that the side chain gave rise to an insignificant impact on absorption, aggregation and photostability in chlorobenzene solution and energy levels but a non‐negligible influence on absorption, photostability and aggregation behavior in the film state. It was found that PIDTT‐DTNT‐C16 with the densest and most ordered packing structure exhibited the best photostability. Inverted bulk heterojunction polymer solar cells based on PIDTT‐DTNT‐HD:PC61BM ([6,6]‐phenyl‐C61‐butyric acid methyl ester) showed at least a 1.5‐fold increase in power conversion efficiency, chiefly originating from its slightly improved absorption, more balanced μh/μe ratio and favorable morphology of the active layer as a result of incorporating branched HD side chains into the IDTT‐alt‐DTNT backbone. © 2019 Society of Chemical Industry