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α,ω-diperfluorohexylquaterthiophene (DFH-4T) has been an attractive n-type material employed in the development of high-mobility organic field-effect transistors. This paper presents a systematic study of the relationship between DFH-4T transistor performance and film structure properties as controlled by deposited thickness. When the DFH-4T thickness increases from 8 nm to 80 nm, the room-temperature field-effect mobility increases monotonically from 0.01 to 1 cm2·V−1·s−1, while the threshold voltage shows a different trend of first decrease then increase. The morphology of thin films revealed by atomic force microscopy shows a dramatic change from multilayered terrace to stacked rod like structures as the film thickness is increased. Yet the crystallite structure and the orientation of molecular constituent, as determined by X-ray diffraction and near-edge X-ray absorption fine structure respectively, do not differ much with respect to film thickness increase. Further analyses of low-temperature transport measurements with mobility-edge model demonstrate that the electronic states of DFH-4T transistors are mainly determined by the film continuity and crystallinity of the bottom multilayered terrace. Moreover, the capacitance-voltage measurements of DFH-4T metal-insulator-semiconductor diodes demonstrate a morphological dependence of charge injection from top contacts, which well explains the variation of threshold voltage with thickness. The overall study provides a deeper understanding of microstructural and molecular growth of DFH-4T film and clarify the structural effects on charge transport and injection for implementation of high-mobility top-contact transistors.