With the aim of enhancing the field‐effect mobility by promoting surface‐mediated two‐dimensional molecular ordering in self‐aligned regioregular poly(3‐hexylthiophene) (P3HT) we have controlled the intermolecular interaction at the interface between P3HT and the insulator substrate by using self‐assembled monolayers (SAMs) functionalized with various groups (–NH2, –OH, and –CH3). We have found that, depending on the properties of the substrate surface, the P3HT nanocrystals adopt two different orientations—parallel and perpendicular to the insulator substrate—which have field‐effect mobilities that differ by more than a factor of 4, and that are as high as 0.28 cm2 V–1 s–1. This surprising increase in field‐effect mobility arises in particular for the perpendicular orientation of the nanocrystals with respect to the insulator substrate. Further, the perpendicular orientation of P3HT nanocrystals can be explained by the following factors: the unshared electron pairs of the SAM end groups, the π–H interactions between the thienyl‐backbone bearing π‐systems and the H (hydrogen) atoms of the SAM end groups, and interdigitation between the alkyl chains of P3HT and the alkyl chains of the SAMs.