Three novel series of transparent fluorinated thermoplastic polyurethane (FTPU) elastomers based on 3-isocyanatomethyl-3,5,5-trimethylcyclohexyl isocyanate (IPDI), polytetramethylene glycol (PTMG), polycaprolactone (PCL) and 4,4-[2,2,2-trifluoro-1-(trifluoromethyl)ethylidene] bisphenol (BPAF) were synthesized by two-step solution polymerization. The FTPU were characterized by Fourier transform infrared spectrometry (FTIR), UV-Visible spectrometry (UV-Vis), wide angle X-ray diffraction (WAXD), atomic force microscopy (AFM), thermogravimetric analysis (TGA), and mechanical tests. The FTIR results indicate that the micro-phase separation and hydrogen bonding strength increase with increasing fluorine content, which are proved by the results of AFM and WAXD. The UV-Vis tests show high transmittance of FTPU films which is affected by crystallization easily. The TGA and mechanical tests indicate that thermal stability and mechanical properties of FTPU are improved significantly with the introduction of BPAF.