Achieving low-power, high-mobility organic thin-film transistors requires control over the buried interface between the semiconductor and the dielectric layers. Here, we demonstrate that siloxane-based molecular design provides a powerful means of engineering interfacial compatibility and charge transport. By integrating siloxane-functionalized diketopyrrolopyrrole (DPP) semiconductors with a PDMS-based polyionic liquid (PIL) dielectric, we show that siloxane–siloxane interactions promote enhanced molecular ordering, increased crystal coherence, and improved charge-carrier mobility of the semiconductor. Grazing-incidence wide-angle X-ray scattering and Raman morphological analyses indicate that interfacial interactions drive coherent stacking and reduce the level of disorder at the interface. This interfacial design strategy offers a general approach to tuning interfaces through conjugated polymer/dielectric systems, offering insight into strategies for the development of low-voltage, high-performance organic electronics.