Fluorinated conjugated polymers have been widely used in high performance polymer solar cells, but they showed limited application in field-effect transistors (FETs). In this paper, we focus on the influence of fluorine atoms upon charge transport of conjugated polymers in FET devices. Two series of conjugated polymers without or with fluorine atoms were designed and applied into FETs. Nonfluorinated conjugated polymers show high hole mobilties up to 11.16 cm(2) V-1 s(1), while fluorinated polymers exhibit low hole mobilities below 1.80 cm(2) V-1 s(1). Further investigation by differential scanning calorimetry (DSC) and 2D grazing-incidence wide-angle X-ray scattering (2D-GIWAXS) reveal that fluorinated conjugated polymers show low crystallinity and face-on orientation in thin films, explaining their poor hole mobilities in FET devices. Our results clearly show how the chemical structures influence the charge transport properties, which can be used to design new conjugated polymers toward high performance FETs.