Three series of quinoxaline-based liquid crystal materials with or without semifluorinated alkyl chains have been successfully synthesized. Their thermal stabilities, reduction potentials, and mesophase characteristics have been examined by TGA, CV, POM, DSC, and temperature-dependent PXRD, respectively. The molecular orientation and their film morphology on the substrate (SiO2/Si) with or without SAMs also have investigated by PXRD and AFM. The control of molecular orientation, to be perpendicular to the substrate treated with PFTS via fluorophilic/fluorophobic interaction, has been achieved. This method provides a new molecular design principle enabling desired molecular alignment of organic semiconducting materials for organic field-effect transistors.