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Side-chain sequence enabled regioisomeric acceptors, bearing different side-chain sequences on the same conjugated backbone, are herein reported. Two regioregular polymers PTBI-1 and PTBI-2 and one regiorandom polymer PTBI-3 were synthesized from these two regioisomeric acceptors for a comparative study. UV–vis–NIR absorption spectroscopy and electrochemical study confirmed similar frontier molecular orbital levels of the three polymers in their solid state. More intriguingly, absorption profiles suggest that the sequence of side chains greatly governs the aggregation behaviors. Furthermore, the PTBI-2 film shows larger ordered domains than PTBI-1 and PTBI-3 films, as supported by AFM and GIWAXS measurements. As a result, PTBI-2-based FET devices achieved an average hole mobility of 1.37 cm2 V–1 s–1, much higher than the two polymers with other side-chain sequences. The regiorandom PTBI-3 exhibited the lowest average hole mobility of 0.27 cm2 V–1 s–1. This study highlights the significant impact of side-chain sequence regioisomerism on aggregation behaviors, morphologies, and subsequently charge transport properties of donor–acceptor type conjugated polymers.