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Temperature‐dependent (80–350 K) charge transport in polymer semiconductor thin films is studied in parallel with in situ X‐ray structural characterization at equivalent temperatures. The study is conducted on a pair of isoindigo‐based polymers containing the same π‐conjugated backbone with different side chains: one with siloxane‐terminated side chains (PII2T‐Si) and the other with branched alkyl‐terminated side chains (PII2T‐Ref). The different chemical moiety in the side chain results in a completely different film morphology. PII2T‐Si films show domains of both edge‐on and face‐on orientations (bimodal orientation) while PII2T‐Ref films show domains of edge‐on orientation (unimodal orientation). Electrical transport properties of this pair of polymers are also distinctive, especially at high temperatures (>230 K). Smaller activation energy (E _A) and larger pre‐exponential factor (μ ₀) in the mobility …