Organic semiconductors are well-known to exhibit high charge carrier mobility based on their spread of the π-orbital. In particular, the π-orbital overlap between neighboring molecules significantly affects their charge carrier mobility. This study elucidated the direct effect of subtle differences in the π-orbital overlap on charge carrier mobility, by precisely controlling only molecular arrangements without any chemical modifications. We synthesized disulfonic acid composed of a [1]benzothieno[3,2-b][1]benzothiophene (BTBT) moiety, and prepared organic salts with four butylamine isomers. Regardless of the type of butylamine combined, electronic states of the constituent BTBT derivative were identical, and all BTBT arrangements were edge-to-face herringbone-type. However, depending on the difference of steric hindrance, center-to-center distances and dihedral angles between neighboring BTBT moieties slightly varied. Despite a similar arrangement, the photoconductivity of four organic salts differed by a factor of approximately two. Additionally, theoretical charge carrier mobilities from their crystal structures exhibited a strong correlation with their photoconductivity.