Understanding the structure and configurations of small-molecule organic semiconductor (OSC) materials is essential in modifying their material properties. Here, we use density functional theory (DFT) to explore the impact of intramolecular noncovalent interactions on the isomerization and structure of the benzodithiophene (BDT) trimer. Fluorine substitutions modify the dihedral coupling between BDTs on the same molecule, thereby significantly increases charge mobility up to 13.2 cm 2 V −1 s −1 . In the fluorinated isomers, the formation of hydrogen bonds overcomes the repulsive S•••S interaction in the syn-conformer, leading to a more planar backbone structure. To validate the DFT simulations, we simulated inelastic neutron scattering (INS) spectroscopy of different anti-and syn-isomers in mixed configuration crystals and compared them to measured INS. Two main messages emerge from this study. (1) Although the through space interaction of fluorine with sulfur is the main contributor to dihedral planarization, H-bonding formed through selective fluorination plays a critical role. (2) A crystal structure that includes a mixture of several configurations could have significant mobility, while the dihedral disorder is mitigated by configurations that are energetically very similar. Our investigation reveals that both syn-and anti-conformers are common in the BDT-trimer crystal, demonstrating that isomeric or configuration purity is not a prerequisite for high charge mobility over 10 cm 2 V −1 s −1 . This work provides a fundamental understanding of the interplay between intramolecular interactions, isomerization, and side chain effects in OSC materials, guiding the design of new generations of OSC materials.